为什么做这件事？ 初衷是用于做基因的注释，后来发现有些数据库多多少少有些问题，比如基因名错了、基因ID过时了等等，为了方便重复使用数据库，所以将常用的数据库整理好了，方便重复调用。数据库预处理的原则是简单又灵活。
软件功能： 基因水平的注释。
library(devtools)
options(options(timeout = max(600, getOption("timeout")))) # install size about 500Mb
install_github("fentouxungui/BiologyDB")如果下载不下来，建议下载Release里的文件，然后本地安装。
如果仅仅是使用整理好的数据，建议安装fentouxungui/BiologyDBLight包。
library(devtools)
install_github("fentouxungui/BiologyDBLight")首先，由于各种各样的原因，并非所有的数据都整理的很好【更新到最新ID】。另外，建议在注释本地数据时，先更新本地基因数据到最新的ID。
-
人的话，用HGNC提供的在线工具Multi-symbol checker进行更新，然后用ZhangRtools包里的 Check_hgnc_hits 对匹配结果预处理。gtf version: Gencode v47
-
小鼠的话，用MGI提供的在线工具MGI Batch Query进行基因ID更新。gtf version: Gencode vM36
-
果蝇的话，用Flybase提供的在线工具Batch Download或ID Validator进行ID更新。gtf version: flybase r6.62
library(BiologyDBLight)
d <- data(package = "BiologyDB")
all_data <- d$results[,"Item"]
print(all_data)
#> [1] "AnimalTFDB_Fly_TF"
#> [2] "AnimalTFDB_Fly_TFCofactors"
#> [3] "AnimalTFDB_Human_TF"
#> [4] "AnimalTFDB_Human_TFCofactors"
#> [5] "AnimalTFDB_Mouse_TF"
#> [6] "AnimalTFDB_Mouse_TFCofactors"
#> [7] "CellChat_Human_Ligand_Receptors_Interactions"
#> [8] "CellChat_Human_Ligands"
#> [9] "CellChat_Human_Receptors"
#> [10] "CellChat_Mouse_LigandReceptorsInteractions"
#> [11] "CellChat_Mouse_Ligands"
#> [12] "CellChat_Mouse_Receptors"
#> [13] "CellPhoneDB_Human_Interactions"
#> [14] "CellPhoneDB_Human_Ligands"
#> [15] "CellPhoneDB_Human_Receptors"
#> [16] "CellTalkDB_Human_Interactions"
#> [17] "CellTalkDB_Mouse_Interactions"
#> [18] "Flybase_Fly_AutomatedGeneSummary"
#> [19] "Flybase_Fly_BestGeneSummary"
#> [20] "Flybase_Fly_GeneSnapshots"
#> [21] "Flybase_Fly_Genes"
#> [22] "GENCODE_Human_Genes"
#> [23] "GENCODE_Mouse_Genes"
#> [24] "GENEONTOLOGY_Fly"
#> [25] "GENEONTOLOGY_Human"
#> [26] "GENEONTOLOGY_Mouse"
#> [27] "HPA_Human_AllGenes_GO_Disease_Distribution_Location"
#> [28] "HPA_Human_CDmarker_Genes"
#> [29] "HPA_Human_FDA_Approved_Secreted_Genes"
#> [30] "HPA_Human_FDA_approved_drug_target_genes"
#> [31] "HPA_Human_GPCRs_Genes"
#> [32] "HPA_Human_Plasma_Genes"
#> [33] "HPA_Human_Predicted_Secreted_Genes"
#> [34] "HPA_Human_Predicted_membrane_Genes"
#> [35] "HPA_Human_ProteinClass_TranscriptionFactors"
#> [36] "HPA_Human_Transporter_Genes"
#> [37] "Human_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull"
#> [38] "Human_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull_Expanded"
#> [39] "Human_GuideToPHARMACOLOGY_Interactions_OnlyTargetsFull_Expanded"
#> [40] "Human_GuideToPHARMACOLOGY_LigandsPeptides"
#> [41] "Human_GuideToPHARMACOLOGY_Targets"
#> [42] "Mouse_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull"
#> [43] "Mouse_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull_Expanded"
#> [44] "Mouse_GuideToPHARMACOLOGY_Interactions_OnlyTargetsFull_Expanded"
#> [45] "Mouse_GuideToPHARMACOLOGY_LigandsPeptides"
#> [46] "Mouse_GuideToPHARMACOLOGY_Targets"
#> [47] "NCBI_Human_GeneSummary"
#> [48] "NCBI_Mouse_GeneSummary"
#> [49] "TheHumanTranscriptionFactors"
#> [50] "UniProt_Human_GeneFunction"
#> [51] "UniProt_Mouse_GeneFunction"
#> [52] "UniProt_ProteinFamily_AllSpecies"
#> [53] "UniProt_ProteinFamily_Human"
#> [54] "UniProt_ProteinFamily_Mouse"
#> [55] "VerSeDa_Mouse_SecretomePrediction"for (i in all_data) {
print(paste0( paste0(rep('#', 20), collapse = ''), ' ',i, ' ',paste0(rep('#', 20), collapse = '')))
print(str(get(i)))
}
#> [1] "#################### AnimalTFDB_Fly_TF ####################"
#> 'data.frame': 651 obs. of 5 variables:
#> $ Ensembl : chr "FBgn0004896" "FBgn0262582" "FBgn0040466" "FBgn0000439" ...
#> $ Entrez_ID : int 37631 53560 40579 40832 38005 41395 34847 41069 42390 31741 ...
#> $ Entrez_latest: chr "37631" "53560" "40579" "40832" ...
#> $ Symbol : chr "fd59A" "cic" "Dlip2" "Dfd" ...
#> $ Family : chr "Fork_head" "HMG" "THAP" "Homeobox" ...
#> NULL
#> [1] "#################### AnimalTFDB_Fly_TFCofactors ####################"
#> 'data.frame': 375 obs. of 5 variables:
#> $ Ensembl : chr "FBgn0000042" "FBgn0000057" "FBgn0000083" "FBgn0000117" ...
#> $ Entrez : int 31521 37073 42492 31151 42936 41446 45827 39744 39340 32078 ...
#> $ Symbol : chr "Act5C" "adp" "AnxB9" "arm" ...
#> $ Family : chr "Actin" "WD" "Others" "Casein" ...
#> $ EntrezID: chr "31521" "37073" "42492" "31151" ...
#> NULL
#> [1] "#################### AnimalTFDB_Human_TF ####################"
#> 'data.frame': 1659 obs. of 5 variables:
#> $ Ensembl : chr "ENSG00000123268" "ENSG00000254553" "ENSG00000134595" "ENSG00000269404" ...
#> $ Entrez : int 466 NA 6658 6689 253639 7768 3239 9572 22887 84327 ...
#> $ Symbol : chr "ATF1" "ENSG00000254553" "SOX3" "SPIB" ...
#> $ Family : chr "TF_bZIP" "ZBTB" "HMG" "ETS" ...
#> $ EntrezID: chr "466" NA "6658" "6689" ...
#> NULL
#> [1] "#################### AnimalTFDB_Human_TFCofactors ####################"
#> 'data.frame': 1024 obs. of 5 variables:
#> $ Ensembl : chr "ENSG00000004487" "ENSG00000004975" "ENSG00000005100" "ENSG00000005302" ...
#> $ Entrez : int 23028 1856 56919 10943 1387 55904 23077 80853 54623 51188 ...
#> $ Symbol : chr "KDM1A" "DVL2" "DHX33" "MSL3" ...
#> $ Family : chr "Lysine demethylase" "Others" "RNA helicase" "Others" ...
#> $ EntrezID: chr "23028" "1856" "56919" "10943" ...
#> NULL
#> [1] "#################### AnimalTFDB_Mouse_TF ####################"
#> 'data.frame': 1611 obs. of 5 variables:
#> $ Ensembl : chr "ENSMUSG00000063804" "ENSMUSG00000000093" "ENSMUSG00000042508" "ENSMUSG00000021604" ...
#> $ Entrez_ID: int 380669 21385 23857 50916 54131 665001 668501 100041433 16363 22764 ...
#> $ Symbol : chr "Lin28b" "Tbx2" "Dmtf1" "Irx4" ...
#> $ Family : chr "CSD" "T-box" "MYB" "Homeobox" ...
#> $ Entrez : chr "380669" "21385" "23857" "50916" ...
#> NULL
#> [1] "#################### AnimalTFDB_Mouse_TFCofactors ####################"
#> 'data.frame': 970 obs. of 5 variables:
#> $ Ensembl : chr "ENSMUSG00000000085" "ENSMUSG00000000275" "ENSMUSG00000000441" "ENSMUSG00000000561" ...
#> $ Entrez_ID: int 29871 217069 110157 70465 11991 57316 16950 12231 18519 20587 ...
#> $ Symbol : chr "Scmh1" "Trim25" "Raf1" "Wdr77" ...
#> $ Family : chr "Others" "Tripartite motif" "Others" "WD" ...
#> $ Entrez : chr "29871" "217069" "110157" "70465" ...
#> NULL
#> [1] "#################### CellChat_Human_Ligand_Receptors_Interactions ####################"
#> 'data.frame': 3227 obs. of 29 variables:
#> $ interaction_name : chr "TGFB1_TGFBR1_TGFBR2" "TGFB2_TGFBR1_TGFBR2" "TGFB3_TGFBR1_TGFBR2" "TGFB1_ACVR1B_TGFBR2" ...
#> $ pathway_name : chr "TGFb" "TGFb" "TGFb" "TGFb" ...
#> $ ligand : chr "TGFB1" "TGFB2" "TGFB3" "TGFB1" ...
#> $ receptor : chr "TGFbR1_R2" "TGFbR1_R2" "TGFbR1_R2" "ACVR1B_TGFbR2" ...
#> $ agonist : chr "TGFb agonist" "TGFb agonist" "TGFb agonist" "TGFb agonist" ...
#> $ antagonist : chr "TGFb antagonist" "TGFb antagonist" "TGFb antagonist" "TGFb antagonist" ...
#> $ co_A_receptor : chr "" "" "" "" ...
#> $ co_I_receptor : chr "TGFb inhibition receptor" "TGFb inhibition receptor" "TGFb inhibition receptor" "TGFb inhibition receptor" ...
#> $ evidence : chr "KEGG: hsa04350" "KEGG: hsa04350" "KEGG: hsa04350" "PMID: 27449815" ...
#> $ annotation : chr "Secreted Signaling" "Secreted Signaling" "Secreted Signaling" "Secreted Signaling" ...
#> $ interaction_name_2 : chr "TGFB1 - (TGFBR1+TGFBR2)" "TGFB2 - (TGFBR1+TGFBR2)" "TGFB3 - (TGFBR1+TGFBR2)" "TGFB1 - (ACVR1B+TGFBR2)" ...
#> $ is_neurotransmitter : logi FALSE FALSE FALSE FALSE FALSE FALSE ...
#> $ ligand.symbol : chr "TGFB1" "TGFB2" "TGFB3" "TGFB1" ...
#> $ ligand.family : chr "TGF-beta" "TGF-beta" "TGF-beta" "TGF-beta" ...
#> $ ligand.location : chr "Extracellular matrix, Secreted, Extracellular space" "Extracellular matrix, Secreted, Extracellular space" "Extracellular matrix, Secreted, Extracellular space" "Extracellular matrix, Secreted, Extracellular space" ...
#> $ ligand.keyword : chr "Disease variant, Signal, Reference proteome, Extracellular matrix, Disulfide bond, Secreted, Mitogen, Growth fa"| __truncated__ "Disease variant, Chromosomal rearrangement, Signal, Reference proteome, Disulfide bond, Secreted, Extracellular"| __truncated__ "Disease variant, Signal, Reference proteome, Extracellular matrix, Disulfide bond, Secreted, Mitogen, Cardiomyo"| __truncated__ "Disease variant, Signal, Reference proteome, Extracellular matrix, Disulfide bond, Secreted, Mitogen, Growth fa"| __truncated__ ...
#> $ ligand.secreted_type : chr "growth factor" "growth factor" "cytokine;growth factor" "growth factor" ...
#> $ ligand.transmembrane : logi FALSE FALSE TRUE FALSE FALSE FALSE ...
#> $ receptor.symbol : chr "TGFBR2, TGFBR1" "TGFBR2, TGFBR1" "TGFBR2, TGFBR1" "TGFBR2, ACVR1B" ...
#> $ receptor.family : chr "Protein kinase superfamily, TKL Ser/Thr protein kinase" "Protein kinase superfamily, TKL Ser/Thr protein kinase" "Protein kinase superfamily, TKL Ser/Thr protein kinase" "Protein kinase superfamily, TKL Ser/Thr protein kinase" ...
#> $ receptor.location : chr "Cell membrane, Secreted, Membrane raft, Cell surface, Cell junction, Tight junction" "Cell membrane, Secreted, Membrane raft, Cell surface, Cell junction, Tight junction" "Cell membrane, Secreted, Membrane raft, Cell surface, Cell junction, Tight junction" "Cell membrane, Secreted, Membrane raft" ...
#> $ receptor.keyword : chr "Membrane, Secreted, Disulfide bond, Kinase, Transmembrane, Differentiation, ATP-binding, Receptor, Alternative "| __truncated__ "Membrane, Secreted, Disulfide bond, Kinase, Transmembrane, Differentiation, ATP-binding, Receptor, Alternative "| __truncated__ "Membrane, Secreted, Disulfide bond, Kinase, Transmembrane, Differentiation, ATP-binding, Receptor, Alternative "| __truncated__ "Membrane, Secreted, Disulfide bond, Kinase, Transmembrane, Differentiation, ATP-binding, Receptor, Alternative "| __truncated__ ...
#> $ receptor.surfaceome_main: chr "Receptors" "Receptors" "Receptors" "Receptors" ...
#> $ receptor.surfaceome_sub : chr "Act.TGFB;Kinase" "Act.TGFB;Kinase" "Act.TGFB;Kinase" "Act.TGFB;Kinase" ...
#> $ receptor.adhesome : chr "" "" "" "" ...
#> $ receptor.secreted_type : chr "" "" "" "" ...
#> $ receptor.transmembrane : logi TRUE TRUE TRUE TRUE TRUE TRUE ...
#> $ receptor.Ensembl.Added : chr "ENSG00000163513;ENSG00000106799" "ENSG00000163513;ENSG00000106799" "ENSG00000163513;ENSG00000106799" "ENSG00000163513;ENSG00000135503" ...
#> $ ligand.Ensembl.Added : chr "ENSG00000105329" "ENSG00000092969" "ENSG00000119699" "ENSG00000105329" ...
#> NULL
#> [1] "#################### CellChat_Human_Ligands ####################"
#> 'data.frame': 782 obs. of 3 variables:
#> $ ligand.Ensembl.Added: chr "ENSG00000001617" "ENSG00000002586" "ENSG00000002745" "ENSG00000006128" ...
#> $ pathway_name : chr "SEMA3" "CD99" "WNT" "TAC" ...
#> $ interaction : chr "SEMA3F - (NRP2+PLXNA1);SEMA3F - (NRP2+PLXNA2);SEMA3F - (NRP2+PLXNA3);SEMA3F - (NRP2+PLXNA4)" "CD99 - PILRA;CD99 - CD99;CD99 - CD99L2;Cd99 - Pilrb" "WNT16 - (FZD1+LRP5);WNT16 - (FZD10+LRP5);WNT16 - (FZD2+LRP5);WNT16 - (FZD3+LRP5);WNT16 - (FZD4+LRP5);WNT16 - (F"| __truncated__ "TAC1 - TACR1;TAC1 - TACR2" ...
#> NULL
#> [1] "#################### CellChat_Human_Receptors ####################"
#> 'data.frame': 717 obs. of 3 variables:
#> $ receptor.Ensembl.Added: chr "ENSG00000002586" "ENSG00000004399" "ENSG00000004468" "ENSG00000004948" ...
#> $ pathway_name : chr "CD99" "SEMA3" "PECAM2" "CALCR;ADM;CALC;IAPP" ...
#> $ interaction : chr "CD99 - CD99" "SEMA3C - PLXND1;SEMA3E - PLXND1;SEMA3C - (NRP1+NRP2)" "PECAM1 - CD38" "ADM - CALCR;CALCA - CALCR;CALCB - CALCR;IAPP - CALCR;ADM - (CALCR+RAMP1);ADM - (CALCRL+RAMP1);CALCA - (CALCR+RA"| __truncated__ ...
#> NULL
#> [1] "#################### CellChat_Mouse_LigandReceptorsInteractions ####################"
#> 'data.frame': 3355 obs. of 30 variables:
#> $ interaction_name : chr "TGFB1_TGFBR1_TGFBR2" "TGFB2_TGFBR1_TGFBR2" "TGFB3_TGFBR1_TGFBR2" "TGFB1_ACVR1B_TGFBR2" ...
#> $ pathway_name : chr "TGFb" "TGFb" "TGFb" "TGFb" ...
#> $ ligand : chr "Tgfb1" "Tgfb2" "Tgfb3" "Tgfb1" ...
#> $ receptor : chr "TGFbR1_R2" "TGFbR1_R2" "TGFbR1_R2" "ACVR1B_TGFbR2" ...
#> $ agonist : chr "TGFb agonist" "TGFb agonist" "TGFb agonist" "TGFb agonist" ...
#> $ antagonist : chr "TGFb antagonist" "TGFb antagonist" "TGFb antagonist" "TGFb antagonist" ...
#> $ co_A_receptor : chr "" "" "" "" ...
#> $ co_I_receptor : chr "TGFb inhibition receptor" "TGFb inhibition receptor" "TGFb inhibition receptor" "TGFb inhibition receptor" ...
#> $ evidence : chr "KEGG: mmu04350" "KEGG: mmu04350" "KEGG: mmu04350" "PMID: 27449815" ...
#> $ annotation : chr "Secreted Signaling" "Secreted Signaling" "Secreted Signaling" "Secreted Signaling" ...
#> $ interaction_name_2 : chr "Tgfb1 - (Tgfbr1+Tgfbr2)" "Tgfb2 - (Tgfbr1+Tgfbr2)" "Tgfb3 - (Tgfbr1+Tgfbr2)" "Tgfb1 - (Acvr1b+Tgfbr2)" ...
#> $ is_neurotransmitter : logi FALSE FALSE FALSE FALSE FALSE FALSE ...
#> $ ligand.symbol : chr "Tgfb1" "Tgfb2" "Tgfb3" "Tgfb1" ...
#> $ ligand.family : chr "TGF-beta" "TGF-beta" "TGF-beta" "TGF-beta" ...
#> $ ligand.location : chr "Extracellular matrix, Secreted, Extracellular space" "Extracellular matrix, Secreted, Extracellular space" "Extracellular matrix, Secreted, Extracellular space" "Extracellular matrix, Secreted, Extracellular space" ...
#> $ ligand.keyword : chr "Disease variant, Signal, Reference proteome, Extracellular matrix, Disulfide bond, Secreted, Mitogen, Growth fa"| __truncated__ "Disease variant, Chromosomal rearrangement, Signal, Reference proteome, Disulfide bond, Secreted, Extracellular"| __truncated__ "Disease variant, Signal, Reference proteome, Extracellular matrix, Disulfide bond, Secreted, Mitogen, Cardiomyo"| __truncated__ "Disease variant, Signal, Reference proteome, Extracellular matrix, Disulfide bond, Secreted, Mitogen, Growth fa"| __truncated__ ...
#> $ ligand.secreted_type : chr "growth factor" "growth factor" "cytokine;growth factor" "growth factor" ...
#> $ ligand.transmembrane : logi FALSE FALSE TRUE FALSE FALSE FALSE ...
#> $ receptor.symbol : chr "Tgfbr1, Tgfbr2" "Tgfbr1, Tgfbr2" "Tgfbr1, Tgfbr2" "Acvr1b, Tgfbr2" ...
#> $ receptor.family : chr "Protein kinase superfamily, TKL Ser/Thr protein kinase" "Protein kinase superfamily, TKL Ser/Thr protein kinase" "Protein kinase superfamily, TKL Ser/Thr protein kinase" "Protein kinase superfamily, TKL Ser/Thr protein kinase" ...
#> $ receptor.location : chr "Cell membrane, Secreted, Membrane raft, Cell surface, Cell junction, Tight junction" "Cell membrane, Secreted, Membrane raft, Cell surface, Cell junction, Tight junction" "Cell membrane, Secreted, Membrane raft, Cell surface, Cell junction, Tight junction" "Cell membrane, Secreted, Membrane raft" ...
#> $ receptor.keyword : chr "Membrane, Secreted, Disulfide bond, Kinase, Transmembrane, Differentiation, ATP-binding, Receptor, Alternative "| __truncated__ "Membrane, Secreted, Disulfide bond, Kinase, Transmembrane, Differentiation, ATP-binding, Receptor, Alternative "| __truncated__ "Membrane, Secreted, Disulfide bond, Kinase, Transmembrane, Differentiation, ATP-binding, Receptor, Alternative "| __truncated__ "Membrane, Secreted, Disulfide bond, Kinase, Transmembrane, Differentiation, ATP-binding, Receptor, Alternative "| __truncated__ ...
#> $ receptor.surfaceome_main: chr "Receptors" "Receptors" "Receptors" "Receptors" ...
#> $ receptor.surfaceome_sub : chr "Act.TGFB;Kinase" "Act.TGFB;Kinase" "Act.TGFB;Kinase" "Act.TGFB;Kinase" ...
#> $ receptor.adhesome : chr "" "" "" "" ...
#> $ receptor.secreted_type : chr "" "" "" "" ...
#> $ receptor.transmembrane : logi TRUE TRUE TRUE TRUE TRUE TRUE ...
#> $ version : chr "CellChatDB v1" "CellChatDB v1" "CellChatDB v1" "CellChatDB v1" ...
#> $ receptor.Ensembl : chr "ENSMUSG00000007613;ENSMUSG00000032440" "ENSMUSG00000007613;ENSMUSG00000032440" "ENSMUSG00000007613;ENSMUSG00000032440" "ENSMUSG00000000532;ENSMUSG00000032440" ...
#> $ ligand.Ensembl : chr "ENSMUSG00000002603" "ENSMUSG00000039239" "ENSMUSG00000021253" "ENSMUSG00000002603" ...
#> NULL
#> [1] "#################### CellChat_Mouse_Ligands ####################"
#> 'data.frame': 736 obs. of 3 variables:
#> $ ligand.Ensembl: chr "ENSMUSG00000000125" "ENSMUSG00000000126" "ENSMUSG00000000182" "ENSMUSG00000000183" ...
#> $ pathway_name : chr "WNT" "WNT" "FGF" "FGF" ...
#> $ interaction : chr "Wnt3 - (Fzd1+Lrp5);Wnt3 - (Fzd10+Lrp5);Wnt3 - (Fzd2+Lrp5);Wnt3 - (Fzd3+Lrp5);Wnt3 - (Fzd4+Lrp5);Wnt3 - (F"| __truncated__ "Wnt9a - (Fzd1+Lrp5);Wnt9a - (Fzd10+Lrp5);Wnt9a - (Fzd2+Lrp5);Wnt9a - (Fzd3+Lrp5);Wnt9a - (Fzd4+Lrp5);Wnt9a"| __truncated__ "Fgf23 - Fgfr1;Fgf23 - Fgfr3;Fgf23 - Fgfr4" "Fgf6 - Fgfr1;Fgf6 - Fgfr2;Fgf6 - Fgfr3;Fgf6 - Fgfr4" ...
#> NULL
#> [1] "#################### CellChat_Mouse_Receptors ####################"
#> 'data.frame': 734 obs. of 3 variables:
#> $ receptor.Ensembl: chr "ENSMUSG00000000120" "ENSMUSG00000000157" "ENSMUSG00000000263" "ENSMUSG00000000290" ...
#> $ pathway_name : chr "NGF;NT" "ICAM;JAM;ICAM" "Glycine" "CD40;COMPLEMENT;CD23;GP1BA;ICAM;JAM;THY1;COMPLEMENT;CD23;ICAM;THY1;ICAM;JAM;VCAM" ...
#> $ interaction : chr "Ngf - Ngfr;Klk1b4 - Ngfr;Bdnf - Ngfr;Ntf3 - Ngfr;Ntf5 - Ngfr" "Icam1 - (Itgam+Itgb2l);Icam2 - (Itgam+Itgb2l);Jam3 - (Itgam+Itgb2l);Icam1 - (Itgal+Itgb2l);Icam2 - (Itgal+Itgb2l)" "Gly-(Shmt1+Slc6a5) - (Glra1+Glrb);Gly-(Shmt1+Slc6a9) - (Glra1+Glrb);Gly-(Shmt2+Slc6a5) - (Glra1+Glrb);Gly-(Shmt"| __truncated__ "Cd40lg - (Itgam+Itgb2);C3 - (Itgam+Itgb2);Fcer2a - (Itgam+Itgb2);Gp1ba - (Itgam+Itgb2);Icam1 - (Itgam+Itgb"| __truncated__ ...
#> NULL
#> [1] "#################### CellPhoneDB_Human_Interactions ####################"
#> 'data.frame': 2911 obs. of 13 variables:
#> $ Ligand.Symbol : chr "CDH1" "COL10A1" "COL11A1" "COL11A2" ...
#> $ Receptor.Symbol : chr "ITGB1;ITGA2" "ITGB1;ITGA2" "ITGB1;ITGA2" "ITGB1;ITGA2" ...
#> $ Ligand.Ensembl.Old : chr "ENSG00000039068" "ENSG00000123500" "ENSG00000060718" "ENSG00000235708|ENSG00000206290|ENSG00000230930|ENSG00000204248|ENSG00000227801" ...
#> $ Receptor.Ensembl.Old : chr "ENSG00000150093;ENSG00000164171" "ENSG00000150093;ENSG00000164171" "ENSG00000150093;ENSG00000164171" "ENSG00000150093;ENSG00000164171" ...
#> $ Ligand.Symbol.Latest : chr "CDH1" "COL10A1" "COL11A1" "COL11A2" ...
#> $ Receptor.Symbol.Latest : chr "ITGB1;ITGA2" "ITGB1;ITGA2" "ITGB1;ITGA2" "ITGB1;ITGA2" ...
#> $ Ligand.Ensembl.Latest : chr "ENSG00000039068" "ENSG00000123500" "ENSG00000060718" "ENSG00000204248" ...
#> $ Receptor.Ensembl.Latest: chr "ENSG00000150093;ENSG00000164171" "ENSG00000150093;ENSG00000164171" "ENSG00000150093;ENSG00000164171" "ENSG00000150093;ENSG00000164171" ...
#> $ classification : chr "Adhesion by Cadherin" "Adhesion by Collagen/Integrin" "Adhesion by Collagen/Integrin" "Adhesion by Collagen/Integrin" ...
#> $ source : chr "PMID:12392763" "uniprot" "uniprot" "uniprot" ...
#> $ annotation_strategy : chr "curated" "curated" "curated" "curated" ...
#> $ is_ppi : chr "True" "True" "True" "True" ...
#> $ directionality : chr "Adhesion-Adhesion" "Adhesion-Adhesion" "Adhesion-Adhesion" "Adhesion-Adhesion" ...
#> NULL
#> [1] "#################### CellPhoneDB_Human_Ligands ####################"
#> 'data.frame': 745 obs. of 3 variables:
#> $ Ligand.Ensembl.Latest: chr "ENSG00000001617" "ENSG00000002586" "ENSG00000002745" "ENSG00000006128" ...
#> $ classification : chr "Signaling by Semaphorin" "" "Signaling by WNT" "Signaling by Tachykinins" ...
#> $ Ligand.Symbol.Latest : chr "SEMA3F" "CD99" "WNT16" "TAC1" ...
#> NULL
#> [1] "#################### CellPhoneDB_Human_Receptors ####################"
#> 'data.frame': 671 obs. of 3 variables:
#> $ Receptor.Ensembl.Latest: chr "ENSG00000004399" "ENSG00000004468" "ENSG00000004948" "ENSG00000005844" ...
#> $ classification : chr "Signaling by Semaphorin" "" "Signaling by Amylin" "Adhesion by ICAM" ...
#> $ Receptor.Symbol.Latest : chr "PLXND1" "CD38" "CALCR" "ITGAL" ...
#> NULL
#> [1] "#################### CellTalkDB_Human_Interactions ####################"
#> 'data.frame': 3398 obs. of 11 variables:
#> $ lr_pair : chr "SEMA3F_PLXNA3" "SEMA3F_PLXNA1" "SEMA3F_NRP1" "SEMA3F_NRP2" ...
#> $ ligand_gene_symbol : chr "SEMA3F" "SEMA3F" "SEMA3F" "SEMA3F" ...
#> $ receptor_gene_symbol : chr "PLXNA3" "PLXNA1" "NRP1" "NRP2" ...
#> $ ligand_gene_id : int 6405 6405 6405 6405 6376 50865 50865 50865 50865 1634 ...
#> $ receptor_gene_id : int 55558 5361 8829 8828 1524 150 4543 2359 2917 1956 ...
#> $ ligand_ensembl_protein_id : chr "ENSP00000002829" "ENSP00000002829" "ENSP00000002829" "ENSP00000002829" ...
#> $ receptor_ensembl_protein_id: chr "ENSP00000358696" "ENSP00000377061" "ENSP00000265371" "ENSP00000353582" ...
#> $ ligand_ensembl_gene_id : chr "ENSG00000001617" "ENSG00000001617" "ENSG00000001617" "ENSG00000001617" ...
#> $ receptor_ensembl_gene_id : chr "ENSG00000130827" "ENSG00000114554" "ENSG00000099250" "ENSG00000118257" ...
#> $ evidence : chr "15721238" "26156437" "9883722" "15721238" ...
#> $ label : chr "First" "First" "First" "First" ...
#> NULL
#> [1] "#################### CellTalkDB_Mouse_Interactions ####################"
#> 'data.frame': 2033 obs. of 10 variables:
#> $ lr_pair : chr "Wnt3_Fzd6" "Wnt3_Egfr" "Wnt3_Fzd2" "Wnt3_Lrp5" ...
#> $ ligand_gene_symbol : chr "Wnt3" "Wnt3" "Wnt3" "Wnt3" ...
#> $ receptor_gene_symbol : chr "Fzd6" "Egfr" "Fzd2" "Lrp5" ...
#> $ ligand_gene_id : chr "22415" "22415" "22415" "22415" ...
#> $ receptor_gene_id : chr "14368" "13649" "57265" "16973" ...
#> $ ligand_ensembl_protein_id : chr "ENSMUSP00000000127" "ENSMUSP00000000127" "ENSMUSP00000000127" "ENSMUSP00000000127" ...
#> $ receptor_ensembl_protein_id: chr "ENSMUSP00000022906" "ENSMUSP00000020329" "ENSMUSP00000091463" "ENSMUSP00000025856" ...
#> $ ligand_ensembl_gene_id : chr "ENSMUSG00000000125" "ENSMUSG00000000125" "ENSMUSG00000000125" "ENSMUSG00000000125" ...
#> $ receptor_ensembl_gene_id : chr "ENSMUSG00000022297" "ENSMUSG00000020122" "ENSMUSG00000050288" "ENSMUSG00000024913" ...
#> $ evidence : chr "19901330" "17374561" "31907106" "11719191" ...
#> NULL
#> [1] "#################### Flybase_Fly_AutomatedGeneSummary ####################"
#> 'data.frame': 32148 obs. of 1 variable:
#> $ ## FlyBase automated gene summaries 2025_01: chr "#primary_FBgn\tsummary_text" "FBgn0000001\tThe gene small nuclear RNA 4.5S is referred to in FlyBase by the symbol Dmel\\snRNA:4.5S (FBgn0000"| __truncated__ "FBgn0000002\tThe gene 5S ribosomal RNA is referred to in FlyBase by the symbol Dmel\\5SrRNA (FBgn0000002). This"| __truncated__ "FBgn0000003\tThe gene Signal recognition particle 7SL RNA CR32864 is referred to in FlyBase by the symbol Dmel\"| __truncated__ ...
#> NULL
#> [1] "#################### Flybase_Fly_BestGeneSummary ####################"
#> 'data.frame': 55415 obs. of 1 variable:
#> $ X...FlyBase.Best.Gene.Summary.report: chr "## Generated: Mon Feb 03 10:09:39 2025" "## Using datasource: fb_2025_01_reporting" "## Note: The single best available gene summary is reported for each D. melanogaster gene." "## Note: Gene summaries are taken from the following sources, in order of decreasing rank:" ...
#> NULL
#> [1] "#################### Flybase_Fly_GeneSnapshots ####################"
#> 'data.frame': 13991 obs. of 1 variable:
#> $ ## FlyBase Gene Snapshot Report: chr "## Generated: Mon Feb 3 09:58:52 2025" "## Using datasource: dbi:Pg:dbname=fb_2025_01_reporting;host=flysql25;port=5432..." "## Genes that currently do not have a gene snapshot are included in this file and marked with \"Contributions w"| __truncated__ "##FBgn_ID\tGeneSymbol\tGeneName\tdatestamp\tgene_snapshot_text" ...
#> NULL
#> [1] "#################### Flybase_Fly_Genes ####################"
#> 'data.frame': 17872 obs. of 12 variables:
#> $ Ensembl : chr "FBgn0031081" "FBgn0052826" "FBgn0031085" "FBgn0062565" ...
#> $ Symbol : chr "Nep3" "tRNA:Pro-CGG-1-1" "CG9570" "Or19b" ...
#> $ Gene.Type: Factor w/ 16 levels "gene","mRNA",..: 1 1 1 1 1 1 1 1 1 1 ...
#> $ EntrezID : chr "33005" "3772294" "33009" "260693" ...
#> $ Name : chr "Neprilysin 3" "transfer RNA:Proline-CGG 1-1" "uncharacterized protein" "Odorant receptor 19b" ...
#> $ Alias : chr "CEC" "AE002611.trna1-ProCGG" "Dmel\\CG9570" "CG32825" ...
#> $ UniProt : chr "Q8SWS1" NA "Q9W5X6" "Q8IRZ5" ...
#> $ Chrosome : Factor w/ 25 levels "2L","2R","3L",..: 6 6 6 6 6 6 6 6 6 6 ...
#> $ Start : int 19961297 20025099 20051294 20094398 20133579 20141819 20110110 20091428 20000968 19958393 ...
#> $ End : int 19969323 20025170 20052519 20095767 20138878 20143188 20110575 20092408 20002096 19959403 ...
#> $ Length : int 8027 72 1226 1370 5300 1370 466 981 1129 1011 ...
#> $ Strand : Factor w/ 3 levels "+","-","*": 1 1 1 1 1 2 2 2 2 2 ...
#> NULL
#> [1] "#################### GENCODE_Human_Genes ####################"
#> 'data.frame': 78724 obs. of 13 variables:
#> $ Ensembl : chr "ENSG00000290825" "ENSG00000223972" "ENSG00000310526" "ENSG00000227232" ...
#> $ Symbol : chr "DDX11L16" "DDX11L1" "WASH7P" "WASH7P" ...
#> $ HGNC : chr NA "37102" "38034" "38034" ...
#> $ Gene.Type: chr "lncRNA" "transcribed_unprocessed_pseudogene" "lncRNA" "transcribed_unprocessed_pseudogene" ...
#> $ EntrezID : chr "84771" NA NA NA ...
#> $ Name : chr "DEAD/H-box helicase 11 like 2 (pseudogene)" NA NA NA ...
#> $ Alias : chr "DDX11L2" NA NA NA ...
#> $ UniProt : chr NA NA NA NA ...
#> $ Chrosome : Factor w/ 25 levels "chr1","chr2",..: 1 1 1 1 1 1 1 1 1 1 ...
#> $ Start : int 11121 12010 14356 14696 17369 28589 30366 34553 36526 51891 ...
#> $ End : int 24894 13670 30744 24886 17436 31109 30503 37595 40778 64116 ...
#> $ Length : int 13774 1661 16389 10191 68 2521 138 3043 4253 12226 ...
#> $ Strand : Factor w/ 3 levels "+","-","*": 1 1 2 2 2 1 1 2 1 1 ...
#> NULL
#> [1] "#################### GENCODE_Mouse_Genes ####################"
#> 'data.frame': 78239 obs. of 13 variables:
#> $ Ensembl : chr "ENSMUSG00000102693" "ENSMUSG00000064842" "ENSMUSG00000051951" "ENSMUSG00000102851" ...
#> $ Symbol : chr "4933401J01Rik" "Gm26206" "Xkr4" "Gm18956" ...
#> $ MGI : chr "1918292" "5455983" "3528744" "5011141" ...
#> $ Gene.Type: chr "TEC" "snRNA" "protein_coding" "processed_pseudogene" ...
#> $ EntrezID : chr NA "115487594" "497097" "100418032" ...
#> $ Name : chr NA "predicted gene, 26206" "X-linked Kx blood group related 4" "coenzyme Q2 homolog, prenyltransferase pseudogene" ...
#> $ Alias : chr NA "Gm26206" "Gm210" "Gm18956" ...
#> $ UniProt : chr NA NA "Q5GH67" NA ...
#> $ Chrosome : Factor w/ 22 levels "chr1","chr2",..: 1 1 1 1 1 1 1 1 1 1 ...
#> $ Start : int 3143476 3172239 3276124 3322980 3435954 3445779 3535200 3536794 3582674 3602018 ...
#> $ End : int 3144545 3172348 3741721 3323459 3438772 3448011 3537508 3583776 3584730 3602943 ...
#> $ Length : int 1070 110 465598 480 2819 2233 2309 46983 2057 926 ...
#> $ Strand : Factor w/ 3 levels "+","-","*": 1 1 2 1 2 2 2 1 2 1 ...
#> NULL
#> [1] "#################### GENEONTOLOGY_Fly ####################"
#> 'data.frame': 12667 obs. of 8 variables:
#> $ Ensembl : chr "FBgn0000002" "FBgn0000003" "FBgn0000008" "FBgn0000013" ...
#> $ Symbol : chr "5SrRNA" "7SLRNA:CR32864" "a" "abd" ...
#> $ MolecularFunction_GOID : chr "-" "-" "-" "-" ...
#> $ MolecularFunction_GOName: chr "-" "-" "-" "-" ...
#> $ CellularComponent_GOID : chr "GO:0022625" "GO:0005786; GO:0005786" "GO:0016324; GO:0005912" "-" ...
#> $ CellularComponent_GOName: chr "cytosolic large ribosomal subunit" "signal recognition particle, endoplasmic reticulum targeting; signal recognition particle, endoplasmic reticulum targeting" "apical plasma membrane; adherens junction" "-" ...
#> $ BiologicalProcess_GOID : chr "-" "GO:0006614; GO:0006617" "GO:0048749" "GO:0007423" ...
#> $ BiologicalProcess_GOName: chr "-" "SRP-dependent cotranslational protein targeting to membrane; SRP-dependent cotranslational protein targeting to"| __truncated__ "compound eye development" "sensory organ development" ...
#> NULL
#> [1] "#################### GENEONTOLOGY_Human ####################"
#> 'data.frame': 44614 obs. of 8 variables:
#> $ Symbol : chr "19s-20s-pa28ab_human" "19s-20s-pa28g_human" "19s regulatory complex_human" "20s-pa200_human" ...
#> $ MolecularFunction_GOID : chr "GO:0004298; GO:0101005" "GO:0004298; GO:0101005" "GO:0101005" "GO:0004298; GO:0070577" ...
#> $ MolecularFunction_GOName: chr "threonine-type endopeptidase activity; deubiquitinase activity" "threonine-type endopeptidase activity; deubiquitinase activity" "deubiquitinase activity" "threonine-type endopeptidase activity; lysine-acetylated histone binding" ...
#> $ CellularComponent_GOID : chr "GO:0005829" "GO:0005829" "GO:0008021" "GO:0005634" ...
#> $ CellularComponent_GOName: chr "cytosol" "cytosol" "synaptic vesicle" "nucleus" ...
#> $ BiologicalProcess_GOID : chr "GO:0006979; GO:0061136; GO:0071357" "GO:0006979; GO:0061136" "-" "GO:0006281; GO:0006974; GO:0010499" ...
#> $ BiologicalProcess_GOName: chr "response to oxidative stress; regulation of proteasomal protein catabolic process; cellular response to type I interferon" "response to oxidative stress; regulation of proteasomal protein catabolic process" "-" "DNA repair; DNA damage response; proteasomal ubiquitin-independent protein catabolic process" ...
#> $ Ensembl.Latest : chr NA NA NA NA ...
#> NULL
#> [1] "#################### GENEONTOLOGY_Mouse ####################"
#> 'data.frame': 21119 obs. of 9 variables:
#> $ MGI : chr "MGI:101757" "MGI:101758" "MGI:101759" "MGI:101760" ...
#> $ Symbol : chr "Cfl1" "Dcaf8l" "Syt4" "Sfswap" ...
#> $ MolecularFunction_GOID : chr "GO:0003779; GO:0005102; GO:0005515; GO:0019903; GO:0051015; GO:1902936" "-" "GO:0000149; GO:0001786; GO:0005544; GO:0017075; GO:0019905; GO:0030276; GO:0030348; GO:0042803; GO:0046872; GO:"| __truncated__ "GO:0003723; GO:0005515" ...
#> $ MolecularFunction_GOName: chr "actin binding; signaling receptor binding; protein binding; protein phosphatase binding; actin filament binding"| __truncated__ "-" "SNARE binding; phosphatidylserine binding; calcium-dependent phospholipid binding; syntaxin-1 binding; syntaxin"| __truncated__ "RNA binding; protein binding" ...
#> $ CellularComponent_GOID : chr "GO:0005634; GO:0005737; GO:0005856; GO:0005886; GO:0016020; GO:0030027; GO:0030175; GO:0030426; GO:0031252; GO:"| __truncated__ "GO:0005737; GO:0080008" "GO:0005794; GO:0005886; GO:0008021; GO:0016020; GO:0030424; GO:0030425; GO:0030667; GO:0031045; GO:0031410; GO:"| __truncated__ "GO:0005634" ...
#> $ CellularComponent_GOName: chr "nucleus; cytoplasm; cytoskeleton; plasma membrane; membrane; lamellipodium; filopodium; growth cone; cell leadi"| __truncated__ "cytoplasm; Cul4-RING E3 ubiquitin ligase complex" "Golgi apparatus; plasma membrane; synaptic vesicle; membrane; axon; dendrite; secretory granule membrane; dense"| __truncated__ "nucleus" ...
#> $ BiologicalProcess_GOID : chr "GO:0006606; GO:0007010; GO:0007015; GO:0007162; GO:0010592; GO:0010593; GO:0022604; GO:0030042; GO:0030043; GO:"| __truncated__ "-" "GO:0007613; GO:0014049; GO:0014059; GO:0017158; GO:0030100; GO:0030154; GO:0031338; GO:0031339; GO:0033604; GO:"| __truncated__ "GO:0006396; GO:0006397; GO:0008380; GO:0048025; GO:0000395; GO:0000380" ...
#> $ BiologicalProcess_GOName: chr "protein import into nucleus; cytoskeleton organization; actin filament organization; negative regulation of cel"| __truncated__ "-" "memory; positive regulation of glutamate secretion; regulation of dopamine secretion; regulation of calcium ion"| __truncated__ "RNA processing; mRNA processing; RNA splicing; negative regulation of mRNA splicing, via spliceosome; mRNA 5'-s"| __truncated__ ...
#> $ Ensembl.Added : chr "ENSMUSG00000056201" "ENSMUSG00000035395" "ENSMUSG00000024261" "ENSMUSG00000029439" ...
#> NULL
#> [1] "#################### HPA_Human_AllGenes_GO_Disease_Distribution_Location ####################"
#> 'data.frame': 20135 obs. of 17 variables:
#> $ Ensembl : chr "ENSG00000121410" "ENSG00000148584" "ENSG00000175899" "ENSG00000166535" ...
#> $ HPA.Gene : chr "A1BG" "A1CF" "A2M" "A2ML1" ...
#> $ HPA.Uniprot : chr "P04217" "Q9NQ94" "P01023" "A8K2U0" ...
#> $ HPA.Protein.class : chr "Plasma proteins, Predicted intracellular proteins, Predicted secreted proteins" "Predicted intracellular proteins" "Cancer-related genes, Candidate cardiovascular disease genes, Plasma proteins, Predicted secreted proteins" "Disease related genes, Predicted intracellular proteins, Predicted secreted proteins" ...
#> $ HPA.Biological.process : chr "" "mRNA processing" "" "" ...
#> $ HPA.Molecular.function : chr "" "RNA-binding" "Protease inhibitor, Serine protease inhibitor" "Protease inhibitor, Serine protease inhibitor" ...
#> $ HPA.Disease.involvement : chr "" "" "Cancer-related genes" "" ...
#> $ HPA.RNA.tissue.specificity : chr "Tissue enriched" "Tissue enriched" "Tissue enhanced" "Tissue enhanced" ...
#> $ HPA.RNA.tissue.distribution : chr "Detected in single" "Detected in some" "Detected in all" "Detected in some" ...
#> $ HPA.RNA.single.cell.type.specificity : chr "Cell type enhanced" "Cell type enhanced" "Cell type enhanced" "Group enriched" ...
#> $ HPA.RNA.single.cell.type.distribution: chr "Detected in many" "Detected in some" "Detected in many" "Detected in some" ...
#> $ HPA.RNA.cancer.specificity : chr "Cancer enriched" "Cancer enriched" "Low cancer specificity" "Cancer enhanced" ...
#> $ HPA.RNA.cancer.distribution : chr "Detected in single" "Detected in many" "Detected in all" "Detected in many" ...
#> $ HPA.RNA.brain.regional.specificity : chr "Low region specificity" "Not detected" "Low region specificity" "Low region specificity" ...
#> $ HPA.Subcellular.location : chr "" "Nucleoplasm" "" "" ...
#> $ HPA.Subcellular.main.location : chr "" "Nucleoplasm" "" "" ...
#> $ HPA.Secretome.location : chr "Secreted to blood" "" "Secreted to blood" "Secreted in other tissues" ...
#> NULL
#> [1] "#################### HPA_Human_CDmarker_Genes ####################"
#> 'data.frame': 384 obs. of 3 variables:
#> $ Ensembl : chr "ENSG00000085563" "ENSG00000118777" "ENSG00000159640" "ENSG00000213088" ...
#> $ HPA.Gene : chr "ABCB1" "ABCG2" "ACE" "ACKR1" ...
#> $ HPA.Uniprot: chr "P08183" "Q9UNQ0" "P12821" "Q16570" ...
#> NULL
#> [1] "#################### HPA_Human_FDA_Approved_Secreted_Genes ####################"
#> 'data.frame': 120 obs. of 3 variables:
#> $ Ensembl : chr "ENSG00000159640" "ENSG00000014257" "ENSG00000163631" "ENSG00000243480" ...
#> $ HPA.Gene : chr "ACE" "ACP3" "ALB" "AMY2A" ...
#> $ HPA.Uniprot: chr "P12821" "P15309" "P02768" "P04746" ...
#> NULL
#> [1] "#################### HPA_Human_FDA_approved_drug_target_genes ####################"
#> 'data.frame': 854 obs. of 3 variables:
#> $ Ensembl : chr "ENSG00000183044" "ENSG00000165029" "ENSG00000103222" "ENSG00000023839" ...
#> $ HPA.Gene : chr "ABAT" "ABCA1" "ABCC1" "ABCC2" ...
#> $ HPA.Uniprot: chr "P80404" "O95477" "P33527" "Q92887" ...
#> NULL
#> [1] "#################### HPA_Human_GPCRs_Genes ####################"
#> 'data.frame': 743 obs. of 3 variables:
#> $ Ensembl : chr "ENSG00000213088" "ENSG00000144648" "ENSG00000144476" "ENSG00000129048" ...
#> $ HPA.Gene : chr "ACKR1" "ACKR2" "ACKR3" "ACKR4" ...
#> $ HPA.Uniprot: chr "Q16570" "O00590" "P25106" "Q9NPB9" ...
#> NULL
#> [1] "#################### HPA_Human_Plasma_Genes ####################"
#> 'data.frame': 3750 obs. of 3 variables:
#> $ Ensembl : chr "ENSG00000121410" "ENSG00000175899" "ENSG00000127837" "ENSG00000090861" ...
#> $ HPA.Gene : chr "A1BG" "A2M" "AAMP" "AARS1" ...
#> $ HPA.Uniprot: chr "P04217" "P01023" "Q13685" "P49588" ...
#> NULL
#> [1] "#################### HPA_Human_Predicted_Secreted_Genes ####################"
#> 'data.frame': 1894 obs. of 3 variables:
#> $ Ensembl : chr "ENSG00000121410" "ENSG00000175899" "ENSG00000166535" "ENSG00000197953" ...
#> $ HPA.Gene : chr "A1BG" "A2M" "A2ML1" "AADACL2" ...
#> $ HPA.Uniprot: chr "P04217" "P01023" "A8K2U0" "Q6P093" ...
#> NULL
#> [1] "#################### HPA_Human_Predicted_membrane_Genes ####################"
#> 'data.frame': 5568 obs. of 3 variables:
#> $ Ensembl : chr "ENSG00000184389" "ENSG00000128274" "ENSG00000081760" "ENSG00000188984" ...
#> $ HPA.Gene : chr "A3GALT2" "A4GALT" "AACS" "AADACL3" ...
#> $ HPA.Uniprot: chr "U3KPV4" "Q9NPC4" "Q86V21" "Q5VUY0" ...
#> NULL
#> [1] "#################### HPA_Human_ProteinClass_TranscriptionFactors ####################"
#> 'data.frame': 1485 obs. of 3 variables:
#> $ HPA.Ensembl: chr "ENSG00000101126" "ENSG00000101544" "ENSG00000139154" "ENSG00000106546" ...
#> $ HPA.Gene : chr "ADNP" "ADNP2" "AEBP2" "AHR" ...
#> $ HPA.Uniprot: chr "Q9H2P0" "Q6IQ32" "Q6ZN18" "P35869" ...
#> NULL
#> [1] "#################### HPA_Human_Transporter_Genes ####################"
#> 'data.frame': 2137 obs. of 3 variables:
#> $ Ensembl : chr "ENSG00000094914" "ENSG00000103591" "ENSG00000181409" "ENSG00000165029" ...
#> $ HPA.Gene : chr "AAAS" "AAGAB" "AATK" "ABCA1" ...
#> $ HPA.Uniprot: chr "Q9NRG9" "Q6PD74" "Q6ZMQ8" "O95477" ...
#> NULL
#> [1] "#################### Human_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull ####################"
#> tibble [615 × 13] (S3: tbl_df/tbl/data.frame)
#> $ LT_Pair_ID : chr [1:615] "5081_1878" "5183_1385" "4358_80" "836_80" ...
#> $ Target.ID : int [1:615] 1878 1385 80 80 315 315 315 2588 2588 2588 ...
#> $ Target : chr [1:615] "4-1BB" "5-LOX" "ACKR3" "ACKR3" ...
#> $ Target.Ensembl: chr [1:615] "ENSG00000049249" "ENSG00000012779" "ENSG00000144476" "ENSG00000144476" ...
#> $ Target.Symbol : chr [1:615] "TNFRSF9" "ALOX5" "ACKR3" "ACKR3" ...
#> $ Target.Type : chr [1:615] "catalytic_receptor" "enzyme" "gpcr" "gpcr" ...
#> $ Target.Family : chr [1:615] "Tumour necrosis factor (TNF) receptor family" "Lipoxygenases" "Chemokine receptors" "Chemokine receptors" ...
#> $ Ligand.ID : int [1:615] 5081 5183 4358 836 810 811 817 4857 4858 4859 ...
#> $ Ligand : chr [1:615] "4-1BB ligand" "5-LOX activating protein" "CXCL12α" "CXCL11" ...
#> $ Ligand.Ensembl: chr [1:615] "ENSG00000125657" "ENSG00000132965" "ENSG00000107562" "ENSG00000169248" ...
#> $ Ligand.Symbol : chr [1:615] "TNFSF9" "ALOX5AP" "CXCL12" "CXCL11" ...
#> $ Approved : chr [1:615] "false" "false" "false" "false" ...
#> $ Type : chr [1:615] "None" "Activator" "Agonist" "Agonist" ...
#> NULL
#> [1] "#################### Human_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull_Expanded ####################"
#> tibble [866 × 13] (S3: tbl_df/tbl/data.frame)
#> $ LT_Pair_ID : chr [1:866] "10014_3103" "1004_220" "10221_76" "1031_223" ...
#> $ Target.ID : int [1:866] 3103 220 76 223 222 223 224 223 224 109 ...
#> $ Target : chr [1:866] "selectin P (CD62)" "ET<sub>B</sub> receptor" "CCK<sub>1</sub> receptor" "FPR2" ...
#> $ Target.Ensembl: chr [1:866] "ENSG00000174175" "ENSG00000136160" "ENSG00000163394" "ENSG00000171049" ...
#> $ Target.Symbol : chr [1:866] "SELP" "EDNRB" "CCKAR" "FPR2" ...
#> $ Target.Type : chr [1:866] "other_protein" "gpcr" "gpcr" "gpcr" ...
#> $ Target.Family : chr [1:866] "CD molecules" "Endothelin receptors" "Cholecystokinin receptors" "Formylpeptide receptors;Leukotriene receptors" ...
#> $ Ligand.ID : int [1:866] 10014 1004 10221 1031 1044 1044 1044 1047 1047 10539 ...
#> $ Ligand : chr [1:866] "selectin P ligand" "endothelin-3" "CCK-39" "annexin I" ...
#> $ Ligand.Ensembl: chr [1:866] "ENSG00000110876" "ENSG00000124205" "ENSG00000187094" "ENSG00000135046" ...
#> $ Ligand.Symbol : chr [1:866] "SELPLG" "EDN3" "CCK" "ANXA1" ...
#> $ Approved : chr [1:866] "false" "false" "false" "false" ...
#> $ Type : chr [1:866] "None" "Agonist" "Agonist" "Agonist" ...
#> NULL
#> [1] "#################### Human_GuideToPHARMACOLOGY_Interactions_OnlyTargetsFull_Expanded ####################"
#> tibble [3,107 × 7] (S3: tbl_df/tbl/data.frame)
#> $ Ensembl : chr [1:3107] "ENSG00000178394" "ENSG00000135312" "ENSG00000179546" "ENSG00000168830" ...
#> $ HGNC : chr [1:3107] "HTR1A" "HTR1B" "HTR1D" "HTR1E" ...
#> $ Symbol : chr [1:3107] "HTR1A" "HTR1B" "HTR1D" "HTR1E" ...
#> $ Entrez : chr [1:3107] "3350" "3351" "3352" "3354" ...
#> $ Target.ID: chr [1:3107] "1" "2" "3" "4" ...
#> $ Type : chr [1:3107] "gpcr" "gpcr" "gpcr" "gpcr" ...
#> $ Family : chr [1:3107] "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" ...
#> NULL
#> [1] "#################### Human_GuideToPHARMACOLOGY_LigandsPeptides ####################"
#> tibble [465 × 4] (S3: tbl_df/tbl/data.frame)
#> $ Ensembl : chr [1:465] "ENSG00000106804" "ENSG00000135744" "ENSG00000171388" "ENSG00000134443" ...
#> $ Symbol : chr [1:465] "C5" "AGT" "APLN" "GRP" ...
#> $ Ligand.ID: chr [1:465] "573;574;8712" "582;583;585;2504;5138;5368;6065;6894" "599;605;606;3556" "612;3582" ...
#> $ Type : chr [1:465] "Peptide" "Peptide" "Peptide" "Peptide" ...
#> NULL
#> [1] "#################### Human_GuideToPHARMACOLOGY_Targets ####################"
#> tibble [3,099 × 7] (S3: tbl_df/tbl/data.frame)
#> $ Ensembl : chr [1:3099] "ENSG00000178394" "ENSG00000135312" "ENSG00000179546" "ENSG00000168830" ...
#> $ HGNC : chr [1:3099] "5286" "5287" "5289" "5291" ...
#> $ Symbol : chr [1:3099] "HTR1A" "HTR1B" "HTR1D" "HTR1E" ...
#> $ Entrez : chr [1:3099] "3350" "3351" "3352" "3354" ...
#> $ Target.ID: int [1:3099] 1 2 3 4 5 6 7 8 9 10 ...
#> $ Type : chr [1:3099] "gpcr" "gpcr" "gpcr" "gpcr" ...
#> $ Family : chr [1:3099] "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" ...
#> NULL
#> [1] "#################### Mouse_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull ####################"
#> tibble [1,156 × 13] (S3: tbl_df/tbl/data.frame)
#> $ LT_Pair_ID : chr [1:1156] "4_2" "5_2" "128_2" "132_2" ...
#> $ Target.ID : int [1:1156] 2 2 2 2 2 2 2 2 2 5 ...
#> $ Target : chr [1:1156] "5-HT<sub>1B</sub> receptor" "5-HT<sub>1B</sub> receptor" "5-HT<sub>1B</sub> receptor" "5-HT<sub>1B</sub> receptor" ...
#> $ Target.Ensembl: chr [1:1156] "ENSMUSG00000049511" "ENSMUSG00000049511" "ENSMUSG00000049511" "ENSMUSG00000049511" ...
#> $ Target.Symbol : chr [1:1156] "Htr1b" "Htr1b" "Htr1b" "Htr1b" ...
#> $ Target.Type : chr [1:1156] "gpcr" "gpcr" "gpcr" "gpcr" ...
#> $ Target.Family : chr [1:1156] "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" ...
#> $ Ligand.ID : int [1:1156] 4 5 128 132 88 135 127 99 102 261 ...
#> $ Ligand : chr [1:1156] "5-CT" "5-hydroxytryptamine" "5-OH-DPAT" "cyanopindolol" ...
#> $ Ligand.Ensembl: chr [1:1156] NA NA NA NA ...
#> $ Ligand.Symbol : chr [1:1156] NA NA NA NA ...
#> $ Approved : chr [1:1156] "false" "false" "false" "false" ...
#> $ Type : chr [1:1156] "Agonist" "Agonist" "Antagonist" "Antagonist" ...
#> NULL
#> [1] "#################### Mouse_GuideToPHARMACOLOGY_Interactions_LigandTargetsFull_Expanded ####################"
#> tibble [1,168 × 13] (S3: tbl_df/tbl/data.frame)
#> $ LT_Pair_ID : chr [1:1168] "100_435" "10020_2604" "10046_2951" "10047_2951" ...
#> $ Target.ID : int [1:1168] 435 2604 2951 2951 1399 226 2945 584 1400 2970 ...
#> $ Target : chr [1:1168] "K<sub>ir</sub>3.2" "dihydroorotate dehydrogenase (quinone)" "Aryl hydrocarbon receptor" "Aryl hydrocarbon receptor" ...
#> $ Target.Ensembl: chr [1:1168] "ENSMUSG00000043301" "ENSMUSG00000031730" "ENSMUSG00000019256" "ENSMUSG00000019256" ...
#> $ Target.Symbol : chr [1:1168] "Kcnj6" "Dhodh" "Ahr" "Ahr" ...
#> $ Target.Type : chr [1:1168] "vgic" "enzyme" "other_protein" "other_protein" ...
#> $ Target.Family : chr [1:1168] "Inwardly rectifying potassium channels (K<sub>IR</sub>)" "1.-.-.- Oxidoreductases;Nucleoside synthesis and metabolism" "Aryl hydrocarbon receptor" "Aryl hydrocarbon receptor" ...
#> $ Ligand.ID : int [1:1168] 100 10020 10046 10047 10062 10107 10111 10119 10124 10124 ...
#> $ Ligand : chr [1:1168] "thioridazine" "DSM421" "indolo[3,2-b]carbazole" "indole-3-carbinol" ...
#> $ Ligand.Ensembl: chr [1:1168] NA NA NA NA ...
#> $ Ligand.Symbol : chr [1:1168] NA NA NA NA ...
#> $ Approved : chr [1:1168] "true" "false" "false" "false" ...
#> $ Type : chr [1:1168] "Gating inhibitor" "Inhibitor" "Agonist" "Agonist" ...
#> NULL
#> [1] "#################### Mouse_GuideToPHARMACOLOGY_Interactions_OnlyTargetsFull_Expanded ####################"
#> tibble [2,939 × 7] (S3: tbl_df/tbl/data.frame)
#> $ Ensembl : chr [1:2939] "ENSMUSG00000021721" "ENSMUSG00000049511" "ENSMUSG00000070687" "ENSMUSG00000050783" ...
#> $ MGI : chr [1:2939] "Htr1a" "Htr1b" "Htr1d" "Htr1f" ...
#> $ Symbol : chr [1:2939] "Htr1a" "Htr1b" "Htr1d" "Htr1f" ...
#> $ Entrez : chr [1:2939] "15550" "15551" "15552" "15557" ...
#> $ Target.ID: chr [1:2939] "1" "2" "3" "5" ...
#> $ Type : chr [1:2939] "gpcr" "gpcr" "gpcr" "gpcr" ...
#> $ Family : chr [1:2939] "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" "5-Hydroxytryptamine receptors" ...
#> NULL
#> [1] "#################### Mouse_GuideToPHARMACOLOGY_LigandsPeptides ####################"
#> tibble [122 × 4] (S3: tbl_df/tbl/data.frame)
#> $ Ensembl : chr [1:122] "ENSMUSG00000020660" "ENSMUSG00000030790" "ENSMUSG00000054136" "ENSMUSG00000027596" ...
#> $ Symbol : chr [1:122] "Pomc" "Adm" "Adm2" "a" ...
#> $ Ligand.ID: chr [1:122] "1331;1320;3722;3607;1333" "3589" "3590" "1329" ...
#> $ Type : chr [1:122] "Peptide" "Peptide" "Peptide" "Peptide" ...
#> NULL
#> [1] "#################### Mouse_GuideToPHARMACOLOGY_Targets ####################"
#> 'data.frame': 2936 obs. of 7 variables:
#> $ Ensembl : chr "ENSMUSG00000028969" "ENSMUSG00000032547" "ENSMUSG00000038612" "ENSMUSG00000022901" ...
#> $ MGI : chr "101765" "101766" "101769" "101773" ...
#> $ Symbol : chr "Cdk5" "Ryk" "Mcl1" "Cd86" ...
#> $ Entrez : chr "12568" "20187" "17210" "12524" ...
#> $ Target.ID: int 1977 1849 2847 2745 2744 738 2171 2535 347 1416 ...
#> $ Type : chr "enzyme" "catalytic_receptor" "other_protein" "other_protein" ...
#> $ Family : chr "CDK5 subfamily" "Type XV RTKs: RYK" "B-cell lymphoma 2 (Bcl-2) protein family" "CD molecules;Other immune checkpoint proteins" ...
#> NULL
#> [1] "#################### NCBI_Human_GeneSummary ####################"
#> 'data.frame': 152238 obs. of 6 variables:
#> $ EntrezID : chr "2" "9" "10" "12" ...
#> $ Symbol : chr "A1BG" "AA" "NAT1" "NATP" ...
#> $ summary : chr "The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence simil"| __truncated__ "The protein encoded by this gene is a protease inhibitor and cytokine transporter. It uses a bait-and-trap mech"| __truncated__ "This gene is one of two arylamine N-acetyltransferase (NAT) genes in the human genome, and is orthologous to th"| __truncated__ "This gene encodes an enzyme that functions to both activate and deactivate arylamine and hydrazine drugs and ca"| __truncated__ ...
#> $ Ensembl : chr "ENSG00000175899" "ENSG00000171428" "ENSG00000156006" "ENSG00000196136" ...
#> $ HGNC : chr "HGNC:7" "HGNC:7645" "HGNC:7646" "HGNC:16" ...
#> $ Ensembl.By.OrgHSegdb: chr "ENSG00000175899" "ENSG00000171428" "ENSG00000156006" "ENSG00000196136" ...
#> NULL
#> [1] "#################### NCBI_Mouse_GeneSummary ####################"
#> 'data.frame': 64352 obs. of 6 variables:
#> $ EntrezID : chr "11287" "11298" "11302" "11303" ...
#> $ Symbol : chr "a" "Aamp" "Aat2" "Aatk" ...
#> $ summary : chr "On February 19, 2002, this locus was switched from human to mouse. The source accession, Z70200.1, is almost id"| __truncated__ "Enables endopeptidase inhibitor activity. Acts upstream of or within embryo implantation. Located in collagen-c"| __truncated__ "The protein encoded by this gene belongs to the acetyltransferase superfamily. It is the penultimate enzyme in "| __truncated__ "Enables protein tyrosine kinase activity. Acts upstream of or within brain development; neuron apoptotic proces"| __truncated__ ...
#> $ Ensembl : chr "ENSMUSG00000030359" "ENSMUSG00000020804" "ENSMUSG00000025375" "ENSMUSG00000015243" ...
#> $ MGI : chr "MGI:87854" "MGI:1328365" "MGI:1197518" "MGI:99607" ...
#> $ Ensembl.By.OrgHSegdb: chr "ENSMUSG00000030359" "ENSMUSG00000020804" "ENSMUSG00000025375" "ENSMUSG00000015243" ...
#> NULL
#> [1] "#################### TheHumanTranscriptionFactors ####################"
#> 'data.frame': 1637 obs. of 6 variables:
#> $ Ensembl : chr "ENSG00000137203" "ENSG00000008196" "ENSG00000087510" "ENSG00000008197" ...
#> $ HGNC.Symbol: chr "TFAP2A" "TFAP2B" "TFAP2C" "TFAP2D" ...
#> $ Entrez : chr "7020" "7021" "7022" "83741" ...
#> $ TF.DBD : chr "AP-2" "AP-2" "AP-2" "AP-2" ...
#> $ Symbol : chr "TFAP2A" "TFAP2B" "TFAP2C" "TFAP2D" ...
#> $ EntrezID : chr "7020" "7021" "7022" "83741" ...
#> NULL
#> [1] "#################### UniProt_Human_GeneFunction ####################"
#> 'data.frame': 17219 obs. of 6 variables:
#> $ Entry : chr "A0A087X1C5" "A0A0B4J2F0" "A0A0C5B5G6" "A0A0K2S4Q6" ...
#> $ Entry.Name : chr "CP2D7_HUMAN" "PIOS1_HUMAN" "MOTSC_HUMAN" "CD3CH_HUMAN" ...
#> $ Protein.names : chr "Putative cytochrome P450 2D7 (EC 1.14.14.1)" "Protein PIGBOS1 (PIGB opposite strand protein 1)" "Mitochondrial-derived peptide MOTS-c (Mitochondrial open reading frame of the 12S rRNA-c)" "Protein CD300H (CD300 antigen-like family member H)" ...
#> $ FunctionCC : chr "CYP2D7" "PIGBOS1" "MT-RNR1" "CD300H" ...
#> $ Primary.Gene.Names: chr "FUNCTION: May be responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It "| __truncated__ "FUNCTION: Plays a role in regulation of the unfolded protein response triggered by endoplasmic reticulum (ER) s"| __truncated__ "FUNCTION: Regulates insulin sensitivity and metabolic homeostasis (PubMed:25738459, PubMed:33468709). Inhibits "| __truncated__ "FUNCTION: May play an important role in innate immunity by mediating a signal for the production of a neutrophi"| __truncated__ ...
#> $ Ensembl.Latest : chr NA NA NA NA ...
#> NULL
#> [1] "#################### UniProt_Mouse_GeneFunction ####################"
#> 'data.frame': 15138 obs. of 6 variables:
#> $ Entry : chr "A0A087WPF7" "A0A088MLT8" "A0A0B4J1F4" "A0A0B4J1G0" ...
#> $ Entry.Name : chr "AUTS2_MOUSE" "IQIP1_MOUSE" "ARRD4_MOUSE" "FCG3A_MOUSE" ...
#> $ Protein.names : chr "Autism susceptibility gene 2 protein homolog" "IQCJ-SCHIP1 readthrough transcript protein" "Arrestin domain-containing protein 4" "Low affinity immunoglobulin gamma Fc region receptor III-A (IgG Fc receptor III-A) (CD16-2) (FcgammaRIV) (CD antigen CD16a)" ...
#> $ FunctionCC : chr "Auts2" "Iqcj-Schip1" "Arrdc4" "Fcgr4" ...
#> $ Primary.Gene.Names: chr "FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maint"| __truncated__ "FUNCTION: May play a role in action potential conduction in myelinated cells through the organization of molecu"| __truncated__ "FUNCTION: Functions as an adapter recruiting ubiquitin-protein ligases to their specific substrates (PubMed:274"| __truncated__ "FUNCTION: Receptor for the invariable Fc fragment of immunoglobulin gamma (IgG) (PubMed:16039578). Binds with i"| __truncated__ ...
#> $ Ensembl.Added : chr NA NA NA NA ...
#> NULL
#> [1] "#################### UniProt_ProteinFamily_AllSpecies ####################"
#> List of 12277
#> $ 'GDSL' lipolytic enzyme family :'data.frame': 146 obs. of 4 variables:
#> ..$ Gene : chr [1:146] "AAE" "AAE" "ACHE" "APG2" ...
#> ..$ Species: chr [1:146] "RAUSE" "RAUVE" "MAIZE" "ARATH" ...
#> ..$ Protein: chr [1:146] "Q3MKY2" "P86830" "B4FZ87" "Q9LU14" ...
#> ..$ family : chr [1:146] "'GDSL' lipolytic enzyme family" "'GDSL' lipolytic enzyme family" "'GDSL' lipolytic enzyme family" "'GDSL' lipolytic enzyme family" ...
#> $ 'GDSL' lipolytic enzyme family. IAH1 subfamily :'data.frame': 7 obs. of 4 variables:
#> ..$ Gene : chr [1:7] "IAH1" "IAH1" "IAH1" "IAH1" ...
#> ..$ Species: chr [1:7] "BOVIN" "DANRE" "HUMAN" "MOUSE" ...
#> ..$ Protein: chr [1:7] "Q3SZ16" "Q503L4" "Q2TAA2" "Q9DB29" ...
#> ..$ family : chr [1:7] "'GDSL' lipolytic enzyme family. IAH1 subfamily" "'GDSL' lipolytic enzyme family. IAH1 subfamily" "'GDSL' lipolytic enzyme family. IAH1 subfamily" "'GDSL' lipolytic enzyme family. IAH1 subfamily" ...
#> $ 'GDSL' lipolytic enzyme family. Phospholipase B1 subfamily :'data.frame': 6 obs. of 4 variables:
#> ..$ Gene : chr [1:6] "PLB1" "PLB1" "PLB1" "PLB1" ...
#> ..$ Species: chr [1:6] "CAVPO" "HUMAN" "MONDO" "MOUSE" ...
#> ..$ Protein: chr [1:6] "O70320" "Q6P1J6" "Q06HQ7" "Q3TTY0" ...
#> ..$ family : chr [1:6] "'GDSL' lipolytic enzyme family. Phospholipase B1 subfamily" "'GDSL' lipolytic enzyme family. Phospholipase B1 subfamily" "'GDSL' lipolytic enzyme family. Phospholipase B1 subfamily" "'GDSL' lipolytic enzyme family. Phospholipase B1 subfamily" ...
#> $ 'GDSL' lipolytic enzyme family. Platelet-activating factor acetylhydrolase IB beta/gamma subunits subfamily :'data.frame': 12 obs. of 4 variables:
#> ..$ Gene : chr [1:12] "PA1B2" "PA1B2" "PA1B2" "PA1B2" ...
#> ..$ Species: chr [1:12] "BOVIN" "CHICK" "DROME" "HUMAN" ...
#> ..$ Protein: chr [1:12] "P68401" "Q5ZMS2" "Q9VXP4" "P68402" ...
#> ..$ family : chr [1:12] "'GDSL' lipolytic enzyme family. Platelet-activating factor acetylhydrolase IB beta/gamma subunits subfamily" "'GDSL' lipolytic enzyme family. Platelet-activating factor acetylhydrolase IB beta/gamma subunits subfamily" "'GDSL' lipolytic enzyme family. Platelet-activating factor acetylhydrolase IB beta/gamma subunits subfamily" "'GDSL' lipolytic enzyme family. Platelet-activating factor acetylhydrolase IB beta/gamma subunits subfamily" ...
#> $ 'GDXG' lipolytic enzyme family :'data.frame': 114 obs. of 4 variables:
#> ..$ Gene : chr [1:114] "AAAD" "AAAD" "AAAD" "AAAD" ...
#> ..$ Species: chr [1:114] "BOVIN" "HUMAN" "MOUSE" "RABIT" ...
#> ..$ Protein: chr [1:114] "Q0P5B7" "P22760" "Q99PG0" "Q7M370" ...
#> ..$ family : chr [1:114] "'GDXG' lipolytic enzyme family" "'GDXG' lipolytic enzyme family" "'GDXG' lipolytic enzyme family" "'GDXG' lipolytic enzyme family" ...
#> $ 'phage' integrase family :'data.frame': 114 obs. of 4 variables:
#> ..$ Gene : chr [1:114] "FIMB" "FIMB" "FIME" "FIME" ...
#> ..$ Species: chr [1:114] "ECO57" "ECOLI" "ECOL6" "ECOLI" ...
#> ..$ Protein: chr [1:114] "P0ADH6" "P0ADH5" "P0ADH8" "P0ADH7" ...
#> ..$ family : chr [1:114] "'phage' integrase family" "'phage' integrase family" "'phage' integrase family" "'phage' integrase family" ...
#> $ 'phage' integrase family. XerA subfamily :'data.frame': 7 obs. of 4 variables:
#> ..$ Gene : chr [1:7] "XERA" "XERA" "XERA" "XERA" ...
#> ..$ Species: chr [1:7] "METTH" "PYRAB" "PYRFU" "PYRHO" ...
#> ..$ Protein: chr [1:7] "O26979" "Q9V1P5" "Q8TZV9" "O59490" ...
#> ..$ family : chr [1:7] "'phage' integrase family. XerA subfamily" "'phage' integrase family. XerA subfamily" "'phage' integrase family. XerA subfamily" "'phage' integrase family. XerA subfamily" ...
#> $ 'phage' integrase family. XerC subfamily :'data.frame': 199 obs. of 4 variables:
#> ..$ Gene : chr [1:199] "XERC1" "XERC" "XERC" "XERC" ...
#> ..$ Species: chr [1:199] "RALSO" "ACTP7" "ACTSZ" "AGRFC" ...
#> ..$ Protein: chr [1:199] "Q8Y3C8" "B3GZ58" "A6VQS4" "Q8UC70" ...
#> ..$ family : chr [1:199] "'phage' integrase family. XerC subfamily" "'phage' integrase family. XerC subfamily" "'phage' integrase family. XerC subfamily" "'phage' integrase family. XerC subfamily" ...
#> $ 'phage' integrase family. XerD subfamily :'data.frame': 68 obs. of 4 variables:
#> ..$ Gene : chr [1:68] "XERD" "XERD" "XERD" "XERD" ...
#> ..$ Species: chr [1:68] "AGRFC" "ALKHC" "BACSU" "BIFLO" ...
#> ..$ Protein: chr [1:68] "Q8U9U6" "Q9KCP0" "P46352" "Q7ZAP1" ...
#> ..$ family : chr [1:68] "'phage' integrase family. XerD subfamily" "'phage' integrase family. XerD subfamily" "'phage' integrase family. XerD subfamily" "'phage' integrase family. XerD subfamily" ...
#> $ 'phage' integrase family. XerD-like subfamily :'data.frame': 37 obs. of 4 variables:
#> ..$ Gene : chr [1:37] "XERDL" "XERDL" "XERDL" "XERDL" ...
#> ..$ Species: chr [1:37] "LACLA" "LACLM" "LACLS" "STRA1" ...
#> ..$ Protein: chr [1:37] "Q9CG32" "A2RKH4" "Q02YQ7" "Q3JZT9" ...
#> ..$ family : chr [1:37] "'phage' integrase family. XerD-like subfamily" "'phage' integrase family. XerD-like subfamily" "'phage' integrase family. XerD-like subfamily" "'phage' integrase family. XerD-like subfamily" ...
#> $ 'phage' integrase family. XerH subfamily :'data.frame': 2 obs. of 4 variables:
#> ..$ Gene : chr [1:2] "XERH" "XERH"
#> ..$ Species: chr [1:2] "CAMJE" "HELPY"
#> ..$ Protein: chr [1:2] "Q0PA27" "O25386"
#> ..$ family : chr [1:2] "'phage' integrase family. XerH subfamily" "'phage' integrase family. XerH subfamily"
#> $ 'phage' integrase family. XerS subfamily :'data.frame': 41 obs. of 4 variables:
#> ..$ Gene : chr [1:41] "XERS" "XERS" "XERS" "XERS" ...
#> ..$ Species: chr [1:41] "LACLA" "LACLM" "LACLS" "STRA1" ...
#> ..$ Protein: chr [1:41] "Q9CG78" "A2RKP9" "Q02YZ4" "Q3K1A9" ...
#> ..$ family : chr [1:41] "'phage' integrase family. XerS subfamily" "'phage' integrase family. XerS subfamily" "'phage' integrase family. XerS subfamily" "'phage' integrase family. XerS subfamily" ...
#> $ 1-acyl-sn-glycerol-3-phosphate acyltransferase family :'data.frame': 92 obs. of 4 variables:
#> ..$ Gene : chr [1:92] "CST26" "GPAT3" "GPAT3" "GPAT3" ...
#> ..$ Species: chr [1:92] "YEAST" "CHICK" "DANRE" "HUMAN" ...
#> ..$ Protein: chr [1:92] "P38226" "Q5ZLL8" "Q6DG38" "Q53EU6" ...
#> ..$ family : chr [1:92] "1-acyl-sn-glycerol-3-phosphate acyltransferase family" "1-acyl-sn-glycerol-3-phosphate acyltransferase family" "1-acyl-sn-glycerol-3-phosphate acyltransferase family" "1-acyl-sn-glycerol-3-phosphate acyltransferase family" ...
#> $ 1-acyl-sn-glycerol-3-phosphate acyltransferase family. OlsA subfamily :'data.frame': 4 obs. of 4 variables:
#> ..$ Gene : chr [1:4] "OLSA" "OLSA" "OLSA" "OLSA"
#> ..$ Species: chr [1:4] "BRUA2" "PSEAE" "RHIME" "RHOCB"
#> ..$ Protein: chr [1:4] "Q2YQS9" "Q9HW50" "Q7APG1" "D5AQD5"
#> ..$ family : chr [1:4] "1-acyl-sn-glycerol-3-phosphate acyltransferase family. OlsA subfamily" "1-acyl-sn-glycerol-3-phosphate acyltransferase family. OlsA subfamily" "1-acyl-sn-glycerol-3-phosphate acyltransferase family. OlsA subfamily" "1-acyl-sn-glycerol-3-phosphate acyltransferase family. OlsA subfamily"
#> $ 11S seed storage protein (globulins) family :'data.frame': 61 obs. of 4 variables:
#> ..$ Gene : chr [1:61] "11S1" "11S1" "11S1" "11S2" ...
#> ..$ Species: chr [1:61] "CARIL" "ELAGV" "MACIN" "ELAGV" ...
#> ..$ Protein: chr [1:61] "B5KVH4" "C0HLM8" "C0HLR7" "C0HLM9" ...
#> ..$ family : chr [1:61] "11S seed storage protein (globulins) family" "11S seed storage protein (globulins) family" "11S seed storage protein (globulins) family" "11S seed storage protein (globulins) family" ...
#> $ 14-3-3 family :'data.frame': 151 obs. of 4 variables:
#> ..$ Gene : chr [1:151] "14310" "14310" "14311" "14312" ...
#> ..$ Species: chr [1:151] "ARATH" "SOLLC" "ARATH" "ARATH" ...
#> ..$ Protein: chr [1:151] "P48347" "P93207" "Q9S9Z8" "Q9C5W6" ...
#> ..$ family : chr [1:151] "14-3-3 family" "14-3-3 family" "14-3-3 family" "14-3-3 family" ...
#> $ 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 family :'data.frame': 16 obs. of 4 variables:
#> ..$ Gene : chr [1:16] "DNPH1" "DNPH1" "DNPH1" "DNPH1" ...
#> ..$ Species: chr [1:16] "BRAFL" "DANRE" "ESOLU" "HUMAN" ...
#> ..$ Protein: chr [1:16] "B6PLN3" "B8A556" "C1BW56" "O43598" ...
#> ..$ family : chr [1:16] "2'-deoxynucleoside 5'-phosphate N-hydrolase 1 family" "2'-deoxynucleoside 5'-phosphate N-hydrolase 1 family" "2'-deoxynucleoside 5'-phosphate N-hydrolase 1 family" "2'-deoxynucleoside 5'-phosphate N-hydrolase 1 family" ...
#> $ 2-5A synthase family :'data.frame': 20 obs. of 4 variables:
#> ..$ Gene : chr [1:20] "OAS1A" "OAS1A" "OAS1B" "OAS1B" ...
#> ..$ Species: chr [1:20] "MOUSE" "RAT" "MOUSE" "RAT" ...
#> ..$ Protein: chr [1:20] "P11928" "Q05961" "Q60856" "Q5BKD0" ...
#> ..$ family : chr [1:20] "2-5A synthase family" "2-5A synthase family" "2-5A synthase family" "2-5A synthase family" ...
#> $ 2-acyl-GPE acetyltransferase family :'data.frame': 56 obs. of 4 variables:
#> ..$ Gene : chr [1:56] "AAS" "AAS" "AAS" "AAS" ...
#> ..$ Species: chr [1:56] "CITK8" "CROS8" "ECO24" "ECO27" ...
#> ..$ Protein: chr [1:56] "A8AP56" "A7MR36" "A7ZQU2" "B7UHQ4" ...
#> ..$ family : chr [1:56] "2-acyl-GPE acetyltransferase family" "2-acyl-GPE acetyltransferase family" "2-acyl-GPE acetyltransferase family" "2-acyl-GPE acetyltransferase family" ...
#> $ 2-aminomuconate deaminase family :'data.frame': 1 obs. of 4 variables:
#> ..$ Gene : chr "AMND"
#> ..$ Species: chr "PSESP"
#> ..$ Protein: chr "Q9KWS2"
#> ..$ family : chr "2-aminomuconate deaminase family"
#> $ 2-oxoacid dehydrogenase family :'data.frame': 118 obs. of 4 variables:
#> ..$ Gene : chr [1:118] "ACOC" "BKDC" "ODB2" "ODB2" ...
#> ..$ Species: chr [1:118] "BACSU" "MYCTU" "ARATH" "BACSU" ...
#> ..$ Protein: chr [1:118] "O31550" "O06159" "Q9M7Z1" "P37942" ...
#> ..$ family : chr [1:118] "2-oxoacid dehydrogenase family" "2-oxoacid dehydrogenase family" "2-oxoacid dehydrogenase family" "2-oxoacid dehydrogenase family" ...
#> $ 2-oxoacid dehydrogenase family. Kgd subfamily :'data.frame': 13 obs. of 4 variables:
#> ..$ Gene : chr [1:13] "KGD" "KGD" "KGD" "KGD" ...
#> ..$ Species: chr [1:13] "MYCBO" "MYCBP" "MYCLE" "MYCPA" ...
#> ..$ Protein: chr [1:13] "Q7U0A6" "A1KI36" "Q9CC97" "Q73WX4" ...
#> ..$ family : chr [1:13] "2-oxoacid dehydrogenase family. Kgd subfamily" "2-oxoacid dehydrogenase family. Kgd subfamily" "2-oxoacid dehydrogenase family. Kgd subfamily" "2-oxoacid dehydrogenase family. Kgd subfamily" ...
#> $ 2-phosphoglycerate kinase family :'data.frame': 13 obs. of 4 variables:
#> ..$ Gene : chr [1:13] "PGK2" "PGK2" "PGK2" "PGK2" ...
#> ..$ Species: chr [1:13] "METFV" "METJA" "METKA" "METM5" ...
#> ..$ Protein: chr [1:13] "Q49156" "Q58877" "Q8TGY9" "A4FW93" ...
#> ..$ family : chr [1:13] "2-phosphoglycerate kinase family" "2-phosphoglycerate kinase family" "2-phosphoglycerate kinase family" "2-phosphoglycerate kinase family" ...
#> $ 2Fe2S plant-type ferredoxin family :'data.frame': 127 obs. of 4 variables:
#> ..$ Gene : chr [1:127] "FDC1" "FDC2" "FER1" "FER1" ...
#> ..$ Species: chr [1:127] "ARATH" "ARATH" "APHFL" "AQUAE" ...
#> ..$ Protein: chr [1:127] "O23344" "Q9C7Y4" "P00244" "O67065" ...
#> ..$ family : chr [1:127] "2Fe2S plant-type ferredoxin family" "2Fe2S plant-type ferredoxin family" "2Fe2S plant-type ferredoxin family" "2Fe2S plant-type ferredoxin family" ...
#> $ 2Fe2S Shethna-type ferredoxin family :'data.frame': 4 obs. of 4 variables:
#> ..$ Gene : chr [1:4] "CBIW" "FER2" "FER2" "FER2"
#> ..$ Species: chr [1:4] "PRIMG" "AQUAE" "AZOVD" "CLOPA"
#> ..$ Protein: chr [1:4] "O87688" "O66511" "P82802" "P07324"
#> ..$ family : chr [1:4] "2Fe2S Shethna-type ferredoxin family" "2Fe2S Shethna-type ferredoxin family" "2Fe2S Shethna-type ferredoxin family" "2Fe2S Shethna-type ferredoxin family"
#> $ 2H phosphoesterase superfamily. CNPase family :'data.frame': 5 obs. of 4 variables:
#> ..$ Gene : chr [1:5] "CN37" "CN37" "CN37" "CN37" ...
#> ..$ Species: chr [1:5] "BOVIN" "HUMAN" "MOUSE" "PONAB" ...
#> ..$ Protein: chr [1:5] "P06623" "P09543" "P16330" "Q5RFD0" ...
#> ..$ family : chr [1:5] "2H phosphoesterase superfamily. CNPase family" "2H phosphoesterase superfamily. CNPase family" "2H phosphoesterase superfamily. CNPase family" "2H phosphoesterase superfamily. CNPase family" ...
#> $ 2H phosphoesterase superfamily. CPD1 family :'data.frame': 11 obs. of 4 variables:
#> ..$ Gene : chr [1:11] "CPD1" "CPD1" "CPD1" "CPD1" ...
#> ..$ Species: chr [1:11] "ASHGO" "CANAL" "CANGA" "DEBHA" ...
#> ..$ Protein: chr [1:11] "Q758H6" "Q59PZ7" "Q6FTX0" "Q6BGW3" ...
#> ..$ family : chr [1:11] "2H phosphoesterase superfamily. CPD1 family" "2H phosphoesterase superfamily. CPD1 family" "2H phosphoesterase superfamily. CPD1 family" "2H phosphoesterase superfamily. CPD1 family" ...
#> $ 2H phosphoesterase superfamily. ThpR family :'data.frame': 12 obs. of 4 variables:
#> ..$ Gene : chr [1:12] "THPR" "THPR" "THPR" "THPR" ...
#> ..$ Species: chr [1:12] "AERPE" "AQUAE" "ARCFU" "BACSU" ...
#> ..$ Protein: chr [1:12] "Q9YB03" "O66967" "O28125" "O34570" ...
#> ..$ family : chr [1:12] "2H phosphoesterase superfamily. ThpR family" "2H phosphoesterase superfamily. ThpR family" "2H phosphoesterase superfamily. ThpR family" "2H phosphoesterase superfamily. ThpR family" ...
#> $ 2H phosphoesterase superfamily. USB1 family :'data.frame': 11 obs. of 4 variables:
#> ..$ Gene : chr [1:11] "USB1" "USB1" "USB1" "USB1" ...
#> ..$ Species: chr [1:11] "BOVIN" "DANRE" "DICDI" "DROME" ...
#> ..$ Protein: chr [1:11] "Q0II50" "Q6DEF6" "Q54W16" "Q9VHB3" ...
#> ..$ family : chr [1:11] "2H phosphoesterase superfamily. USB1 family" "2H phosphoesterase superfamily. USB1 family" "2H phosphoesterase superfamily. USB1 family" "2H phosphoesterase superfamily. USB1 family" ...
#> $ 2H phosphoesterase superfamily. YjcG family :'data.frame': 44 obs. of 4 variables:
#> ..$ Gene : chr [1:44] "Y1009" "Y1013" "Y1015" "Y1020" ...
#> ..$ Species: chr [1:44] "STAA1" "STAA9" "STAAM" "STAAC" ...
#> ..$ Protein: chr [1:44] "A7X0P2" "A5IRJ1" "Q99V77" "Q5HH71" ...
#> ..$ family : chr [1:44] "2H phosphoesterase superfamily. YjcG family" "2H phosphoesterase superfamily. YjcG family" "2H phosphoesterase superfamily. YjcG family" "2H phosphoesterase superfamily. YjcG family" ...
#> $ 2S seed storage albumins family :'data.frame': 49 obs. of 4 variables:
#> ..$ Gene : chr [1:49] "2SS1" "2SS1" "2SS1" "2SS1" ...
#> ..$ Species: chr [1:49] "ARATH" "BEREX" "BRANA" "BRAOA" ...
#> ..$ Protein: chr [1:49] "P15457" "P04403" "P01091" "P84782" ...
#> ..$ family : chr [1:49] "2S seed storage albumins family" "2S seed storage albumins family" "2S seed storage albumins family" "2S seed storage albumins family" ...
#> $ 3-beta-HSD family :'data.frame': 58 obs. of 4 variables:
#> ..$ Gene : chr [1:58] "052L" "3BHS1" "3BHS1" "3BHS1" ...
#> ..$ Species: chr [1:58] "FRG3G" "HUMAN" "MACMU" "MESAU" ...
#> ..$ Protein: chr [1:58] "Q6GZS4" "P14060" "P27365" "Q60555" ...
#> ..$ family : chr [1:58] "3-beta-HSD family" "3-beta-HSD family" "3-beta-HSD family" "3-beta-HSD family" ...
#> $ 3-HAO family :'data.frame': 57 obs. of 4 variables:
#> ..$ Gene : chr [1:57] "3HAO1" "3HAO1" "3HAO1" "3HAO1" ...
#> ..$ Species: chr [1:57] "ASPCL" "ASPFC" "ASPFU" "ASPOR" ...
#> ..$ Protein: chr [1:57] "A1C408" "B0Y9Z9" "Q4WCF1" "Q2UHT9" ...
#> ..$ family : chr [1:57] "3-HAO family" "3-HAO family" "3-HAO family" "3-HAO family" ...
#> $ 3-hydroxyacyl-CoA dehydrogenase family :'data.frame': 244 obs. of 4 variables:
#> ..$ Gene : chr [1:244] "AIM1" "CRYL1" "CRYL1" "CRYL1" ...
#> ..$ Species: chr [1:244] "ARATH" "BOVIN" "HUMAN" "MOUSE" ...
#> ..$ Protein: chr [1:244] "Q9ZPI6" "Q8SPX7" "Q9Y2S2" "Q99KP3" ...
#> ..$ family : chr [1:244] "3-hydroxyacyl-CoA dehydrogenase family" "3-hydroxyacyl-CoA dehydrogenase family" "3-hydroxyacyl-CoA dehydrogenase family" "3-hydroxyacyl-CoA dehydrogenase family" ...
#> $ 3-hydroxyacyl-CoA dehydrogenase family. L-carnitine dehydrogenase subfamily :'data.frame': 17 obs. of 4 variables:
#> ..$ Gene : chr [1:17] "LCDH" "LCDH" "LCDH" "LCDH" ...
#> ..$ Species: chr [1:17] "AGRFC" "BACCZ" "BURMA" "BURPS" ...
#> ..$ Protein: chr [1:17] "Q7D3B2" "Q4V182" "Q62DG4" "Q63MT0" ...
#> ..$ family : chr [1:17] "3-hydroxyacyl-CoA dehydrogenase family. L-carnitine dehydrogenase subfamily" "3-hydroxyacyl-CoA dehydrogenase family. L-carnitine dehydrogenase subfamily" "3-hydroxyacyl-CoA dehydrogenase family. L-carnitine dehydrogenase subfamily" "3-hydroxyacyl-CoA dehydrogenase family. L-carnitine dehydrogenase subfamily" ...
#> $ 3-hydroxybenzoate 6-hydroxylase family :'data.frame': 13 obs. of 4 variables:
#> ..$ Gene : chr [1:13] "3HBH1" "3HBH2" "3HBH" "3HBH" ...
#> ..$ Species: chr [1:13] "PSEAC" "PSEAC" "CORGL" "KLEOX" ...
#> ..$ Protein: chr [1:13] "Q9F131" "Q0QFQ1" "Q8NLB6" "Q5EXK1" ...
#> ..$ family : chr [1:13] "3-hydroxybenzoate 6-hydroxylase family" "3-hydroxybenzoate 6-hydroxylase family" "3-hydroxybenzoate 6-hydroxylase family" "3-hydroxybenzoate 6-hydroxylase family" ...
#> $ 3-oxoacid CoA-transferase family :'data.frame': 14 obs. of 4 variables:
#> ..$ Gene : chr [1:14] "CARA" "SCO2A" "SCO2A" "SCO2B" ...
#> ..$ Species: chr [1:14] "ACEWO" "MOUSE" "RAT" "MOUSE" ...
#> ..$ Protein: chr [1:14] "F1CYZ5" "Q9JJN4" "Q5XIJ9" "Q9ESL0" ...
#> ..$ family : chr [1:14] "3-oxoacid CoA-transferase family" "3-oxoacid CoA-transferase family" "3-oxoacid CoA-transferase family" "3-oxoacid CoA-transferase family" ...
#> $ 3-oxoacid CoA-transferase subunit A family :'data.frame': 20 obs. of 4 variables:
#> ..$ Gene : chr [1:20] "ATOD" "ATOD" "CATI" "CTFA" ...
#> ..$ Species: chr [1:20] "ECOLI" "HAEIN" "PSEKB" "CLOAB" ...
#> ..$ Protein: chr [1:20] "P76458" "P44875" "Q8VPF3" "P33752" ...
#> ..$ family : chr [1:20] "3-oxoacid CoA-transferase subunit A family" "3-oxoacid CoA-transferase subunit A family" "3-oxoacid CoA-transferase subunit A family" "3-oxoacid CoA-transferase subunit A family" ...
#> $ 3-oxoacid CoA-transferase subunit B family :'data.frame': 21 obs. of 4 variables:
#> ..$ Gene : chr [1:21] "ATOA" "ATOA" "CATJ" "CTFB" ...
#> ..$ Species: chr [1:21] "ECOLI" "HAEIN" "PSEKB" "CLOAB" ...
#> ..$ Protein: chr [1:21] "P76459" "P44874" "Q8VPF2" "P23673" ...
#> ..$ family : chr [1:21] "3-oxoacid CoA-transferase subunit B family" "3-oxoacid CoA-transferase subunit B family" "3-oxoacid CoA-transferase subunit B family" "3-oxoacid CoA-transferase subunit B family" ...
#> $ 30 kDa lipoprotein family :'data.frame': 7 obs. of 4 variables:
#> ..$ Gene : chr [1:7] "LP3" "LP4" "LPP12" "LPP19" ...
#> ..$ Species: chr [1:7] "BOMMO" "BOMMO" "BOMMO" "BOMMO" ...
#> ..$ Protein: chr [1:7] "Q00802" "Q00801" "P09335" "P09336" ...
#> ..$ family : chr [1:7] "30 kDa lipoprotein family" "30 kDa lipoprotein family" "30 kDa lipoprotein family" "30 kDa lipoprotein family" ...
#> $ 4-hydroxy-2-oxovalerate aldolase family :'data.frame': 173 obs. of 4 variables:
#> ..$ Gene : chr [1:173] "HOA1" "HOA1" "HOA1" "HOA1" ...
#> ..$ Species: chr [1:173] "AZOSB" "AZOVD" "BURCJ" "BURL3" ...
#> ..$ Protein: chr [1:173] "A1K6L9" "C1DMT5" "B4EK78" "Q397Q9" ...
#> ..$ family : chr [1:173] "4-hydroxy-2-oxovalerate aldolase family" "4-hydroxy-2-oxovalerate aldolase family" "4-hydroxy-2-oxovalerate aldolase family" "4-hydroxy-2-oxovalerate aldolase family" ...
#> $ 4-hydroxybenzoyl-CoA thioesterase family :'data.frame': 18 obs. of 4 variables:
#> ..$ Gene : chr [1:18] "4HBT" "ALT1" "ALT2" "ALT3" ...
#> ..$ Species: chr [1:18] "PSEUC" "ARATH" "ARATH" "ARATH" ...
#> ..$ Protein: chr [1:18] "P56653" "Q9C7I5" "Q9C7I8" "Q8W583" ...
#> ..$ family : chr [1:18] "4-hydroxybenzoyl-CoA thioesterase family" "4-hydroxybenzoyl-CoA thioesterase family" "4-hydroxybenzoyl-CoA thioesterase family" "4-hydroxybenzoyl-CoA thioesterase family" ...
#> $ 4-hydroxybenzoyl-CoA thioesterase family. DHNA-CoA hydrolase subfamily :'data.frame': 34 obs. of 4 variables:
#> ..$ Gene : chr [1:34] "DNAT1" "DNAT2" "DNCH" "DNCH" ...
#> ..$ Species: chr [1:34] "ARATH" "ARATH" "ACAM1" "CROS5" ...
#> ..$ Protein: chr [1:34] "Q9SX65" "Q9FI76" "B0CEN8" "B1WZN0" ...
#> ..$ family : chr [1:34] "4-hydroxybenzoyl-CoA thioesterase family. DHNA-CoA hydrolase subfamily" "4-hydroxybenzoyl-CoA thioesterase family. DHNA-CoA hydrolase subfamily" "4-hydroxybenzoyl-CoA thioesterase family. DHNA-CoA hydrolase subfamily" "4-hydroxybenzoyl-CoA thioesterase family. DHNA-CoA hydrolase subfamily" ...
#> $ 4-oxalocrotonate tautomerase family :'data.frame': 52 obs. of 4 variables:
#> ..$ Gene : chr [1:52] "4OT1" "4OT2" "4OT3" "4OT4" ...
#> ..$ Species: chr [1:52] "PSEPU" "PSEPU" "PSEPU" "PSEPU" ...
#> ..$ Protein: chr [1:52] "Q01468" "Q8RQD2" "Q9Z431" "Q93JW0" ...
#> ..$ family : chr [1:52] "4-oxalocrotonate tautomerase family" "4-oxalocrotonate tautomerase family" "4-oxalocrotonate tautomerase family" "4-oxalocrotonate tautomerase family" ...
#> $ 4-oxalocrotonate tautomerase family. PptA subfamily :'data.frame': 18 obs. of 4 variables:
#> ..$ Gene : chr [1:18] "PPTA" "PPTA" "PPTA" "PPTA" ...
#> ..$ Species: chr [1:18] "CROS8" "ECO24" "ECO27" "ECO57" ...
#> ..$ Protein: chr [1:18] "A7MK78" "A7ZLQ4" "B7URK1" "Q8X9X8" ...
#> ..$ family : chr [1:18] "4-oxalocrotonate tautomerase family. PptA subfamily" "4-oxalocrotonate tautomerase family. PptA subfamily" "4-oxalocrotonate tautomerase family. PptA subfamily" "4-oxalocrotonate tautomerase family. PptA subfamily" ...
#> $ 4-toluene sulfonate uptake permease (TSUP) (TC 2.A.102) family :'data.frame': 26 obs. of 4 variables:
#> ..$ Gene : chr [1:26] "MAMO" "MAMO" "TAUE1" "TAUE2" ...
#> ..$ Species: chr [1:26] "MAGGM" "MAGSA" "ARATH" "ARATH" ...
#> ..$ Protein: chr [1:26] "Q93DZ1" "Q2W8Q2" "F4I8X6" "Q9SYB0" ...
#> ..$ family : chr [1:26] "4-toluene sulfonate uptake permease (TSUP) (TC 2.A.102) family" "4-toluene sulfonate uptake permease (TSUP) (TC 2.A.102) family" "4-toluene sulfonate uptake permease (TSUP) (TC 2.A.102) family" "4-toluene sulfonate uptake permease (TSUP) (TC 2.A.102) family" ...
#> $ 4E-T/EIF4E-T family :'data.frame': 4 obs. of 4 variables:
#> ..$ Gene : chr [1:4] "4ET" "4ET" "4ET" "CUP"
#> ..$ Species: chr [1:4] "DROME" "HUMAN" "MOUSE" "DROME"
#> ..$ Protein: chr [1:4] "Q8IH18" "Q9NRA8" "Q9EST3" "Q9VMA3"
#> ..$ family : chr [1:4] "4E-T/EIF4E-T family" "4E-T/EIF4E-T family" "4E-T/EIF4E-T family" "4E-T/EIF4E-T family"
#> $ 4Fe4S bacterial-type ferredoxin family. RnfB subfamily :'data.frame': 108 obs. of 4 variables:
#> ..$ Gene : chr [1:108] "RNFB" "RNFB" "RNFB" "RNFB" ...
#> ..$ Species: chr [1:108] "ACEWD" "AERHH" "AERS4" "ALCBS" ...
#> ..$ Protein: chr [1:108] "H6LC27" "A0KLJ3" "A4SNP6" "Q0VP40" ...
#> ..$ family : chr [1:108] "4Fe4S bacterial-type ferredoxin family. RnfB subfamily" "4Fe4S bacterial-type ferredoxin family. RnfB subfamily" "4Fe4S bacterial-type ferredoxin family. RnfB subfamily" "4Fe4S bacterial-type ferredoxin family. RnfB subfamily" ...
#> $ 4Fe4S bacterial-type ferredoxin family. RnfC subfamily :'data.frame': 74 obs. of 4 variables:
#> ..$ Gene : chr [1:74] "RNFC" "RNFC" "RNFC" "RNFC" ...
#> ..$ Species: chr [1:74] "ACEWD" "ACTSZ" "BUCAI" "BUCBP" ...
#> ..$ Protein: chr [1:74] "H6LC32" "A6VQ42" "P57215" "Q89AW8" ...
#> ..$ family : chr [1:74] "4Fe4S bacterial-type ferredoxin family. RnfC subfamily" "4Fe4S bacterial-type ferredoxin family. RnfC subfamily" "4Fe4S bacterial-type ferredoxin family. RnfC subfamily" "4Fe4S bacterial-type ferredoxin family. RnfC subfamily" ...
#> $ 4HPPD family :'data.frame': 39 obs. of 4 variables:
#> ..$ Gene : chr [1:39] "HMAS" "HPDL" "HPDL" "HPDL" ...
#> ..$ Species: chr [1:39] "AMYOR" "DICDI" "HUMAN" "MOUSE" ...
#> ..$ Protein: chr [1:39] "O52791" "Q557J8" "Q96IR7" "Q8K248" ...
#> ..$ family : chr [1:39] "4HPPD family" "4HPPD family" "4HPPD family" "4HPPD family" ...
#> $ 5'(3')-deoxyribonucleotidase family :'data.frame': 46 obs. of 4 variables:
#> ..$ Gene : chr [1:46] "53DR" "53DR" "53DR" "53DR" ...
#> ..$ Species: chr [1:46] "BACSU" "BORBR" "BORPA" "BORPE" ...
#> ..$ Protein: chr [1:46] "P68522" "Q7WQA0" "Q7WC96" "Q7W066" ...
#> ..$ family : chr [1:46] "5'(3')-deoxyribonucleotidase family" "5'(3')-deoxyribonucleotidase family" "5'(3')-deoxyribonucleotidase family" "5'(3')-deoxyribonucleotidase family" ...
#> $ 5'-3' exonuclease family :'data.frame': 7 obs. of 4 variables:
#> ..$ Gene : chr [1:7] "EX0N" "EXON" "XRN1" "XRN1" ...
#> ..$ Species: chr [1:7] "IIV3" "IIV6" "HUMAN" "MOUSE" ...
#> ..$ Protein: chr [1:7] "Q197A1" "Q9QSK5" "Q8IZH2" "P97789" ...
#> ..$ family : chr [1:7] "5'-3' exonuclease family" "5'-3' exonuclease family" "5'-3' exonuclease family" "5'-3' exonuclease family" ...
#> $ 5'-3' exonuclease family. XRN2/RAT1 subfamily :'data.frame': 27 obs. of 4 variables:
#> ..$ Gene : chr [1:27] "XRN2" "XRN2" "XRN2" "XRN2" ...
#> ..$ Species: chr [1:27] "ARATH" "ASHGO" "ASPFU" "ASPOR" ...
#> ..$ Protein: chr [1:27] "Q9FQ02" "Q74ZA0" "Q8TFZ1" "Q2UCP5" ...
#> ..$ family : chr [1:27] "5'-3' exonuclease family. XRN2/RAT1 subfamily" "5'-3' exonuclease family. XRN2/RAT1 subfamily" "5'-3' exonuclease family. XRN2/RAT1 subfamily" "5'-3' exonuclease family. XRN2/RAT1 subfamily" ...
#> $ 5'-AMP-activated protein kinase beta subunit family :'data.frame': 18 obs. of 4 variables:
#> ..$ Gene : chr [1:18] "AAKB1" "AAKB1" "AAKB1" "AAKB1" ...
#> ..$ Species: chr [1:18] "BOVIN" "HUMAN" "MOUSE" "PIG" ...
#> ..$ Protein: chr [1:18] "Q5BIS9" "Q9Y478" "Q9R078" "P80387" ...
#> ..$ family : chr [1:18] "5'-AMP-activated protein kinase beta subunit family" "5'-AMP-activated protein kinase beta subunit family" "5'-AMP-activated protein kinase beta subunit family" "5'-AMP-activated protein kinase beta subunit family" ...
#> $ 5'-AMP-activated protein kinase gamma subunit family :'data.frame': 21 obs. of 4 variables:
#> ..$ Gene : chr [1:21] "AAKG1" "AAKG1" "AAKG1" "AAKG1" ...
#> ..$ Species: chr [1:21] "BOVIN" "HUMAN" "MOUSE" "PIG" ...
#> ..$ Protein: chr [1:21] "P58108" "P54619" "O54950" "Q09138" ...
#> ..$ family : chr [1:21] "5'-AMP-activated protein kinase gamma subunit family" "5'-AMP-activated protein kinase gamma subunit family" "5'-AMP-activated protein kinase gamma subunit family" "5'-AMP-activated protein kinase gamma subunit family" ...
#> $ 5'-nucleotidase family :'data.frame': 31 obs. of 4 variables:
#> ..$ Gene : chr [1:31] "5NTD" "5NTD" "5NTD" "5NTD" ...
#> ..$ Species: chr [1:31] "BOVIN" "DIPOM" "HAEIN" "HUMAN" ...
#> ..$ Protein: chr [1:31] "Q05927" "P29240" "P44569" "P21589" ...
#> ..$ family : chr [1:31] "5'-nucleotidase family" "5'-nucleotidase family" "5'-nucleotidase family" "5'-nucleotidase family" ...
#> $ 5'-nucleotidase type 3 family :'data.frame': 4 obs. of 4 variables:
#> ..$ Gene : chr [1:4] "5NT1A" "5NT1A" "5NT1B" "5NT1B"
#> ..$ Species: chr [1:4] "HUMAN" "MOUSE" "HUMAN" "MOUSE"
#> ..$ Protein: chr [1:4] "Q9BXI3" "A3KFX0" "Q96P26" "Q91YE9"
#> ..$ family : chr [1:4] "5'-nucleotidase type 3 family" "5'-nucleotidase type 3 family" "5'-nucleotidase type 3 family" "5'-nucleotidase type 3 family"
#> $ 5-formyltetrahydrofolate cyclo-ligase family :'data.frame': 17 obs. of 4 variables:
#> ..$ Gene : chr [1:17] "5FCLL" "5FCL" "5FCL" "5FCL" ...
#> ..$ Species: chr [1:17] "ARATH" "ARATH" "ECO57" "ECOLI" ...
#> ..$ Protein: chr [1:17] "Q9SRE0" "Q8L539" "P0AC29" "P0AC28" ...
#> ..$ family : chr [1:17] "5-formyltetrahydrofolate cyclo-ligase family" "5-formyltetrahydrofolate cyclo-ligase family" "5-formyltetrahydrofolate cyclo-ligase family" "5-formyltetrahydrofolate cyclo-ligase family" ...
#> $ 5DNU family :'data.frame': 69 obs. of 4 variables:
#> ..$ Gene : chr [1:69] "5DNU" "5DNU" "5DNU" "5DNU" ...
#> ..$ Species: chr [1:69] "CITK8" "CROS8" "ECO24" "ECO27" ...
#> ..$ Protein: chr [1:69] "A8ADU7" "A7MH33" "A7ZPA5" "B7UFU9" ...
#> ..$ family : chr [1:69] "5DNU family" "5DNU family" "5DNU family" "5DNU family" ...
#> $ 6-hydroxynicotinate 3-monooxygenase family :'data.frame': 3 obs. of 4 variables:
#> ..$ Gene : chr [1:3] "6HN3M" "6HN3M" "6HN3M"
#> ..$ Species: chr [1:3] "BORBR" "PSEFL" "PSEPK"
#> ..$ Protein: chr [1:3] "A0A0H3LKL4" "P86491" "Q88FY2"
#> ..$ family : chr [1:3] "6-hydroxynicotinate 3-monooxygenase family" "6-hydroxynicotinate 3-monooxygenase family" "6-hydroxynicotinate 3-monooxygenase family"
#> $ 6-phosphogluconate dehydrogenase family :'data.frame': 66 obs. of 4 variables:
#> ..$ Gene : chr [1:66] "6PGD1" "6PGD1" "6PGD1" "6PGD1" ...
#> ..$ Species: chr [1:66] "ARATH" "ORYSJ" "SPIOL" "YEAST" ...
#> ..$ Protein: chr [1:66] "Q9SH69" "Q9LI00" "Q94KU1" "P38720" ...
#> ..$ family : chr [1:66] "6-phosphogluconate dehydrogenase family" "6-phosphogluconate dehydrogenase family" "6-phosphogluconate dehydrogenase family" "6-phosphogluconate dehydrogenase family" ...
#> $ 7 kDa DNA-binding/endoribonuclease P2 family :'data.frame': 14 obs. of 4 variables:
#> ..$ Gene : chr [1:14] "DN7A" "DN7A" "DN7A" "DN7A" ...
#> ..$ Species: chr [1:14] "ACIHW" "SACS2" "SACSH" "SULID" ...
#> ..$ Protein: chr [1:14] "F4B991" "P61991" "P61990" "D2PHL8" ...
#> ..$ family : chr [1:14] "7 kDa DNA-binding/endoribonuclease P2 family" "7 kDa DNA-binding/endoribonuclease P2 family" "7 kDa DNA-binding/endoribonuclease P2 family" "7 kDa DNA-binding/endoribonuclease P2 family" ...
#> $ 7B2 family :'data.frame': 6 obs. of 4 variables:
#> ..$ Gene : chr [1:6] "7B2" "7B2" "7B2" "7B2" ...
#> ..$ Species: chr [1:6] "HUMAN" "MOUSE" "PANTR" "PIG" ...
#> ..$ Protein: chr [1:6] "P05408" "P12961" "A5A6J6" "P01165" ...
#> ..$ family : chr [1:6] "7B2 family" "7B2 family" "7B2 family" "7B2 family" ...
#> $ 7S seed storage protein family :'data.frame': 49 obs. of 4 variables:
#> ..$ Gene : chr [1:49] "ALL11" "ALL12" "AMP21" "AMP22" ...
#> ..$ Species: chr [1:49] "ARAHY" "ARAHY" "MACIN" "MACIN" ...
#> ..$ Protein: chr [1:49] "P43237" "P43238" "Q9SPL5" "Q9SPL4" ...
#> ..$ family : chr [1:49] "7S seed storage protein family" "7S seed storage protein family" "7S seed storage protein family" "7S seed storage protein family" ...
#> $ A.longa ORF167/ORF288 family :'data.frame': 6 obs. of 4 variables:
#> ..$ Gene : chr [1:6] "YCY1" "YCY2" "YCY3" "YCY4" ...
#> ..$ Species: chr [1:6] "EUGLO" "EUGLO" "EUGLO" "EUGLO" ...
#> ..$ Protein: chr [1:6] "P34775" "P34776" "P58147" "P58149" ...
#> ..$ family : chr [1:6] "A.longa ORF167/ORF288 family" "A.longa ORF167/ORF288 family" "A.longa ORF167/ORF288 family" "A.longa ORF167/ORF288 family" ...
#> $ A9/FIL1 family :'data.frame': 14 obs. of 4 variables:
#> ..$ Gene : chr [1:14] "108" "A9" "A9" "DIRL1" ...
#> ..$ Species: chr [1:14] "SOLLC" "ARATH" "BRANA" "ARATH" ...
#> ..$ Protein: chr [1:14] "Q43495" "Q00762" "Q05772" "Q8W453" ...
#> ..$ family : chr [1:14] "A9/FIL1 family" "A9/FIL1 family" "A9/FIL1 family" "A9/FIL1 family" ...
#> $ AAA ATPase family :'data.frame': 565 obs. of 4 variables:
#> ..$ Gene : chr [1:565] "AFG31" "AFG32" "AFG32" "AFG32" ...
#> ..$ Species: chr [1:565] "MOUSE" "BOVIN" "HUMAN" "MOUSE" ...
#> ..$ Protein: chr [1:565] "Q920A7" "Q2KJI7" "Q9Y4W6" "Q8JZQ2" ...
#> ..$ family : chr [1:565] "AAA ATPase family" "AAA ATPase family" "AAA ATPase family" "AAA ATPase family" ...
#> $ AAA ATPase family. AFG2 subfamily :'data.frame': 10 obs. of 4 variables:
#> ..$ Gene : chr [1:10] "AFG2H" "AFG2" "AFG2" "SPA5L" ...
#> ..$ Species: chr [1:10] "CAEEL" "SCHPO" "YEAST" "BOVIN" ...
#> ..$ Protein: chr [1:10] "Q21222" "O60058" "P32794" "A7YSY2" ...
#> ..$ family : chr [1:10] "AAA ATPase family. AFG2 subfamily" "AAA ATPase family. AFG2 subfamily" "AAA ATPase family. AFG2 subfamily" "AAA ATPase family. AFG2 subfamily" ...
#> $ AAA ATPase family. BCS1 subfamily :'data.frame': 31 obs. of 4 variables:
#> ..$ Gene : chr [1:31] "AATP1" "AATP2" "AATP3" "AATP4" ...
#> ..$ Species: chr [1:31] "ARATH" "ARATH" "ARATH" "ARATH" ...
#> ..$ Protein: chr [1:31] "Q9LP11" "F4IQG2" "Q8GW96" "F4IJ77" ...
#> ..$ family : chr [1:31] "AAA ATPase family. BCS1 subfamily" "AAA ATPase family. BCS1 subfamily" "AAA ATPase family. BCS1 subfamily" "AAA ATPase family. BCS1 subfamily" ...
#> $ AAA ATPase family. CDC48 subfamily :'data.frame': 7 obs. of 4 variables:
#> ..$ Gene : chr [1:7] "CDCH" "SAV" "TERA1" "TERA2" ...
#> ..$ Species: chr [1:7] "HALSA" "SULAC" "CAEEL" "CAEEL" ...
#> ..$ Protein: chr [1:7] "Q9HPF0" "Q07590" "P54811" "P54812" ...
#> ..$ family : chr [1:7] "AAA ATPase family. CDC48 subfamily" "AAA ATPase family. CDC48 subfamily" "AAA ATPase family. CDC48 subfamily" "AAA ATPase family. CDC48 subfamily" ...
#> $ AAA ATPase family. DRC11 subfamily :'data.frame': 3 obs. of 4 variables:
#> ..$ Gene : chr [1:3] "DRC11" "DRC11" "DRC11"
#> ..$ Species: chr [1:3] "CHLRE" "HUMAN" "MOUSE"
#> ..$ Protein: chr [1:3] "A8IHT2" "Q86XH1" "Q9CUL5"
#> ..$ family : chr [1:3] "AAA ATPase family. DRC11 subfamily" "AAA ATPase family. DRC11 subfamily" "AAA ATPase family. DRC11 subfamily"
#> $ AAA ATPase family. Katanin p60 subunit A1 subfamily :'data.frame': 12 obs. of 4 variables:
#> ..$ Gene : chr [1:12] "KTNA1" "KTNA1" "KTNA1" "KTNA1" ...
#> ..$ Species: chr [1:12] "ARATH" "CAEEL" "CHICK" "DANRE" ...
#> ..$ Protein: chr [1:12] "Q9SEX2" "P34808" "Q1HGK7" "Q5RII9" ...
#> ..$ family : chr [1:12] "AAA ATPase family. Katanin p60 subunit A1 subfamily" "AAA ATPase family. Katanin p60 subunit A1 subfamily" "AAA ATPase family. Katanin p60 subunit A1 subfamily" "AAA ATPase family. Katanin p60 subunit A1 subfamily" ...
#> $ AAA ATPase family. Katanin p60 subunit A1 subfamily. A-like 1 sub-subfamily :'data.frame': 8 obs. of 4 variables:
#> ..$ Gene : chr [1:8] "KATL1" "KATL1" "KATL1" "KATL1" ...
#> ..$ Species: chr [1:8] "DANRE" "HUMAN" "MOUSE" "OTOGA" ...
#> ..$ Protein: chr [1:8] "Q5U3S1" "Q9BW62" "Q8K0T4" "B4USW8" ...
#> ..$ family : chr [1:8] "AAA ATPase family. Katanin p60 subunit A1 subfamily. A-like 1 sub-subfamily" "AAA ATPase family. Katanin p60 subunit A1 subfamily. A-like 1 sub-subfamily" "AAA ATPase family. Katanin p60 subunit A1 subfamily. A-like 1 sub-subfamily" "AAA ATPase family. Katanin p60 subunit A1 subfamily. A-like 1 sub-subfamily" ...
#> $ AAA ATPase family. Katanin p60 subunit A1 subfamily. A-like 2 sub-subfamily :'data.frame': 4 obs. of 4 variables:
#> ..$ Gene : chr [1:4] "KATL2" "KATL2" "KATL2" "KATL2"
#> ..$ Species: chr [1:4] "HUMAN" "MOUSE" "XENLA" "XENTR"
#> ..$ Protein: chr [1:4] "Q8IYT4" "Q9D3R6" "Q3B8D5" "A0JMA9"
#> ..$ family : chr [1:4] "AAA ATPase family. Katanin p60 subunit A1 subfamily. A-like 2 sub-subfamily" "AAA ATPase family. Katanin p60 subunit A1 subfamily. A-like 2 sub-subfamily" "AAA ATPase family. Katanin p60 subunit A1 subfamily. A-like 2 sub-subfamily" "AAA ATPase family. Katanin p60 subunit A1 subfamily. A-like 2 sub-subfamily"
#> $ AAA ATPase family. MSP1 subfamily :'data.frame': 8 obs. of 4 variables:
#> ..$ Gene : chr [1:8] "ATAD1" "ATAD1" "ATAD1" "ATAD1" ...
#> ..$ Species: chr [1:8] "BOVIN" "HUMAN" "MOUSE" "RAT" ...
#> ..$ Protein: chr [1:8] "F6QV99" "Q8NBU5" "Q9D5T0" "Q505J9" ...
#> ..$ family : chr [1:8] "AAA ATPase family. MSP1 subfamily" "AAA ATPase family. MSP1 subfamily" "AAA ATPase family. MSP1 subfamily" "AAA ATPase family. MSP1 subfamily" ...
#> $ AAA ATPase family. PCH2 subfamily :'data.frame': 13 obs. of 4 variables:
#> ..$ Gene : chr [1:13] "PCH2" "PCH2" "PCH2" "PCH2" ...
#> ..$ Species: chr [1:13] "ARATH" "CAEEL" "CANLF" "CHICK" ...
#> ..$ Protein: chr [1:13] "Q8H1F9" "Q09535" "E2R222" "E1C6Q1" ...
#> ..$ family : chr [1:13] "AAA ATPase family. PCH2 subfamily" "AAA ATPase family. PCH2 subfamily" "AAA ATPase family. PCH2 subfamily" "AAA ATPase family. PCH2 subfamily" ...
#> $ AAA ATPase family. RarA/MGS1/WRNIP1 subfamily :'data.frame': 15 obs. of 4 variables:
#> ..$ Gene : chr [1:15] "RARA" "RARA" "RARA" "RARA" ...
#> ..$ Species: chr [1:15] "COXBU" "ECO57" "ECOL6" "ECOLI" ...
#> ..$ Protein: chr [1:15] "P39918" "P0AAZ6" "P0AAZ5" "P0AAZ4" ...
#> ..$ family : chr [1:15] "AAA ATPase family. RarA/MGS1/WRNIP1 subfamily" "AAA ATPase family. RarA/MGS1/WRNIP1 subfamily" "AAA ATPase family. RarA/MGS1/WRNIP1 subfamily" "AAA ATPase family. RarA/MGS1/WRNIP1 subfamily" ...
#> $ AAA ATPase family. Spastin subfamily :'data.frame': 28 obs. of 4 variables:
#> ..$ Gene : chr [1:28] "SPAST" "SPAST" "SPAST" "SPAST" ...
#> ..$ Species: chr [1:28] "ANOGA" "BOVIN" "BRUMA" "CAEBR" ...
#> ..$ Protein: chr [1:28] "Q7QBW0" "A2VDN5" "A8QFF6" "A8XV40" ...
#> ..$ family : chr [1:28] "AAA ATPase family. Spastin subfamily" "AAA ATPase family. Spastin subfamily" "AAA ATPase family. Spastin subfamily" "AAA ATPase family. Spastin subfamily" ...
#> $ AAC(2')-I acetyltransferase family :'data.frame': 6 obs. of 4 variables:
#> ..$ Gene : chr [1:6] "AAC2" "AAC2" "AAC2" "AAC2" ...
#> ..$ Species: chr [1:6] "MYCBO" "MYCFO" "MYCS2" "MYCTO" ...
#> ..$ Protein: chr [1:6] "P0A5N1" "Q49157" "P94968" "P9WQG8" ...
#> ..$ family : chr [1:6] "AAC(2')-I acetyltransferase family" "AAC(2')-I acetyltransferase family" "AAC(2')-I acetyltransferase family" "AAC(2')-I acetyltransferase family" ...
#> $ AAE transporter (TC 2.A.81) family :'data.frame': 35 obs. of 4 variables:
#> ..$ Gene : chr [1:35] "ASPT" "Y1016" "Y1229" "Y1411" ...
#> ..$ Species: chr [1:35] "TETHA" "GEOSL" "BACTN" "PORGI" ...
#> ..$ Protein: chr [1:35] "Q8L3K8" "Q74EE6" "Q8A8D8" "Q7MUS4" ...
#> ..$ family : chr [1:35] "AAE transporter (TC 2.A.81) family" "AAE transporter (TC 2.A.81) family" "AAE transporter (TC 2.A.81) family" "AAE transporter (TC 2.A.81) family" ...
#> $ AAE transporter (TC 2.A.81) family. YbjL subfamily :'data.frame': 77 obs. of 4 variables:
#> ..$ Gene : chr [1:77] "Y1101" "Y1145" "Y1232" "Y1326" ...
#> ..$ Species: chr [1:77] "VIBCM" "VIBCH" "VIBPA" "YERPE" ...
#> ..$ Protein: chr [1:77] "C3LLJ2" "Q9KSW1" "Q87QB8" "Q8ZGH1" ...
#> ..$ family : chr [1:77] "AAE transporter (TC 2.A.81) family. YbjL subfamily" "AAE transporter (TC 2.A.81) family. YbjL subfamily" "AAE transporter (TC 2.A.81) family. YbjL subfamily" "AAE transporter (TC 2.A.81) family. YbjL subfamily" ...
#> $ AAE transporter (TC 2.A.81) family. YidE subfamily :'data.frame': 73 obs. of 4 variables:
#> ..$ Gene : chr [1:73] "Y009" "Y013" "Y013" "Y014" ...
#> ..$ Species: chr [1:73] "DICNV" "KLEP3" "YERPY" "YERPP" ...
#> ..$ Protein: chr [1:73] "A5EX03" "B5XT62" "B1JGZ7" "A4TGM8" ...
#> ..$ family : chr [1:73] "AAE transporter (TC 2.A.81) family. YidE subfamily" "AAE transporter (TC 2.A.81) family. YidE subfamily" "AAE transporter (TC 2.A.81) family. YidE subfamily" "AAE transporter (TC 2.A.81) family. YidE subfamily" ...
#> $ AaeX family :'data.frame': 60 obs. of 4 variables:
#> ..$ Gene : chr [1:60] "AAEX" "AAEX" "AAEX" "AAEX" ...
#> ..$ Species: chr [1:60] "CITK8" "CROS8" "ECO27" "ECO45" ...
#> ..$ Protein: chr [1:60] "A8AQD6" "A7MJB3" "B7UJX4" "B7MC03" ...
#> ..$ family : chr [1:60] "AaeX family" "AaeX family" "AaeX family" "AaeX family" ...
#> $ AAMDC family :'data.frame': 4 obs. of 4 variables:
#> ..$ Gene : chr [1:4] "AAMDC" "AAMDC" "AAMDC" "AAMDC"
#> ..$ Species: chr [1:4] "BOVIN" "DANRE" "HUMAN" "MOUSE"
#> ..$ Protein: chr [1:4] "Q32PA8" "Q502H1" "Q9H7C9" "Q8R0P4"
#> ..$ family : chr [1:4] "AAMDC family" "AAMDC family" "AAMDC family" "AAMDC family"
#> $ AapA toxin family :'data.frame': 2 obs. of 4 variables:
#> ..$ Gene : chr [1:2] "AAPA1" "AAPA3"
#> ..$ Species: chr [1:2] "HELPY" "HELPY"
#> ..$ Protein: chr [1:2] "P0DUM4" "P0DUM5"
#> ..$ family : chr [1:2] "AapA toxin family" "AapA toxin family"
#> $ AAR2 family :'data.frame': 9 obs. of 4 variables:
#> ..$ Gene : chr [1:9] "AAR2" "AAR2" "AAR2" "AAR2" ...
#> ..$ Species: chr [1:9] "BOVIN" "CAEEL" "HUMAN" "MACFA" ...
#> ..$ Protein: chr [1:9] "Q08DJ7" "Q09305" "Q9Y312" "Q4R7D0" ...
#> ..$ family : chr [1:9] "AAR2 family" "AAR2 family" "AAR2 family" "AAR2 family" ...
#> $ AATF family :'data.frame': 21 obs. of 4 variables:
#> ..$ Gene : chr [1:21] "AATF" "AATF" "AATF" "AATF" ...
#> ..$ Species: chr [1:21] "CHICK" "DROME" "HUMAN" "MOUSE" ...
#> ..$ Protein: chr [1:21] "Q5ZIM6" "Q9VM95" "Q9NY61" "Q9JKX4" ...
#> ..$ family : chr [1:21] "AATF family" "AATF family" "AATF family" "AATF family" ...
#> $ AB hydrolase 3 family :'data.frame': 11 obs. of 4 variables:
#> ..$ Gene : chr [1:11] "CNSH" "FDB26" "FDB39" "FSH1" ...
#> ..$ Species: chr [1:11] "PENEN" "FUSPC" "GIBM7" "YEAST" ...
#> ..$ Protein: chr [1:11] "A0A0A2JY30" "K3VZ29" "W7MTJ1" "P38777" ...
#> ..$ family : chr [1:11] "AB hydrolase 3 family" "AB hydrolase 3 family" "AB hydrolase 3 family" "AB hydrolase 3 family" ...
#> $ AB hydrolase superfamily :'data.frame': 176 obs. of 4 variables:
#> ..$ Gene : chr [1:176] "AAMHY" "ABD18" "ABD18" "ABD18" ...
#> ..$ Species: chr [1:176] "RHILO" "HUMAN" "MOUSE" "RAT" ...
#> ..$ Protein: chr [1:176] "Q988D4" "Q0P651" "Q8C1A9" "Q4V7A8" ...
#> ..$ family : chr [1:176] "AB hydrolase superfamily" "AB hydrolase superfamily" "AB hydrolase superfamily" "AB hydrolase superfamily" ...
#> $ AB hydrolase superfamily. AB hydrolase 2 family :'data.frame': 46 obs. of 4 variables:
#> ..$ Gene : chr [1:46] "APT11" "APT12" "APTH1" "APTH1" ...
#> ..$ Species: chr [1:46] "DICDI" "DICDI" "ASHGO" "ASPFU" ...
#> ..$ Protein: chr [1:46] "Q54T49" "Q55FK4" "Q750X7" "Q4WCX7" ...
#> ..$ family : chr [1:46] "AB hydrolase superfamily. AB hydrolase 2 family" "AB hydrolase superfamily. AB hydrolase 2 family" "AB hydrolase superfamily. AB hydrolase 2 family" "AB hydrolase superfamily. AB hydrolase 2 family" ...
#> $ AB hydrolase superfamily. AB hydrolase 4 family :'data.frame': 24 obs. of 4 variables:
#> ..$ Gene : chr [1:24] "ABDH3" "ABH15" "ABH15" "ABH2A" ...
#> ..$ Species: chr [1:24] "CAEEL" "HUMAN" "MOUSE" "DANRE" ...
#> ..$ Protein: chr [1:24] "Q18610" "Q6UXT9" "Q5F2F2" "Q802V6" ...
#> ..$ family : chr [1:24] "AB hydrolase superfamily. AB hydrolase 4 family" "AB hydrolase superfamily. AB hydrolase 4 family" "AB hydrolase superfamily. AB hydrolase 4 family" "AB hydrolase superfamily. AB hydrolase 4 family" ...
#> $ AB hydrolase superfamily. ABHD14 family :'data.frame': 9 obs. of 4 variables:
#> ..$ Gene : chr [1:9] "ABHEA" "ABHEA" "ABHEA" "ABHEA" ...
#> ..$ Species: chr [1:9] "DANRE" "HUMAN" "MOUSE" "RAT" ...
#> ..$ Protein: chr [1:9] "Q1LV46" "Q9BUJ0" "Q922Q6" "Q5I0C4" ...
#> ..$ family : chr [1:9] "AB hydrolase superfamily. ABHD14 family" "AB hydrolase superfamily. ABHD14 family" "AB hydrolase superfamily. ABHD14 family" "AB hydrolase superfamily. ABHD14 family" ...
#> $ AB hydrolase superfamily. ABHD16 family :'data.frame': 9 obs. of 4 variables:
#> ..$ Gene : chr [1:9] "ABHGA" "ABHGA" "ABHGA" "ABHGA" ...
#> ..$ Species: chr [1:9] "BOVIN" "HUMAN" "MACFA" "MOUSE" ...
#> ..$ Protein: chr [1:9] "Q1JPD2" "O95870" "Q4R8P0" "Q9Z1Q2" ...
#> ..$ family : chr [1:9] "AB hydrolase superfamily. ABHD16 family" "AB hydrolase superfamily. ABHD16 family" "AB hydrolase superfamily. ABHD16 family" "AB hydrolase superfamily. ABHD16 family" ...
#> $ AB hydrolase superfamily. ABHD17 family :'data.frame': 19 obs. of 4 variables:
#> ..$ Gene : chr [1:19] "AB17A" "AB17A" "AB17A" "AB17A" ...
#> ..$ Species: chr [1:19] "BOVIN" "HUMAN" "MOUSE" "RAT" ...
#> ..$ Protein: chr [1:19] "Q2HJ19" "Q96GS6" "Q99JW1" "Q5XIJ5" ...
#> ..$ family : chr [1:19] "AB hydrolase superfamily. ABHD17 family" "AB hydrolase superfamily. ABHD17 family" "AB hydrolase superfamily. ABHD17 family" "AB hydrolase superfamily. ABHD17 family" ...
#> $ AB hydrolase superfamily. AKT2 hydrolase family :'data.frame': 6 obs. of 4 variables:
#> ..$ Gene : chr [1:6] "ACT21" "ACT22" "ACT23" "ACTT2" ...
#> ..$ Species: chr [1:6] "ALTAL" "ALTAL" "ALTAL" "ALTAL" ...
#> ..$ Protein: chr [1:6] "C9K1M8" "C9K1M9" "C9K1N0" "C9K1M7" ...
#> ..$ family : chr [1:6] "AB hydrolase superfamily. AKT2 hydrolase family" "AB hydrolase superfamily. AKT2 hydrolase family" "AB hydrolase superfamily. AKT2 hydrolase family" "AB hydrolase superfamily. AKT2 hydrolase family" ...
#> $ AB hydrolase superfamily. Bacterial non-heme haloperoxidase / perhydrolase family :'data.frame': 10 obs. of 4 variables:
#> ..$ Gene : chr [1:10] "BPOA2" "CPOA1" "DCH" "ESTE" ...
#> ..$ Species: chr [1:10] "KITAU" "KITAU" "ACICA" "PSEFL" ...
#> ..$ Protein: chr [1:10] "P29715" "P33912" "Q83WC8" "P22862" ...
#> ..$ family : chr [1:10] "AB hydrolase superfamily. Bacterial non-heme haloperoxidase / perhydrolase family" "AB hydrolase superfamily. Bacterial non-heme haloperoxidase / perhydrolase family" "AB hydrolase superfamily. Bacterial non-heme haloperoxidase / perhydrolase family" "AB hydrolase superfamily. Bacterial non-heme haloperoxidase / perhydrolase family" ...
#> $ AB hydrolase superfamily. BphD family :'data.frame': 9 obs. of 4 variables:
#> ..$ Gene : chr [1:9] "BPHD" "BPHD" "BPHD" "BPHD" ...
#> ..$ Species: chr [1:9] "BURCE" "COMTE" "DELAC" "PARXL" ...
#> ..$ Protein: chr [1:9] "Q2VLB9" "Q59324" "Q8KRD3" "P47229" ...
#> ..$ family : chr [1:9] "AB hydrolase superfamily. BphD family" "AB hydrolase superfamily. BphD family" "AB hydrolase superfamily. BphD family" "AB hydrolase superfamily. BphD family" ...
#> $ AB hydrolase superfamily. Carboxylesterase BioH family :'data.frame': 109 obs. of 4 variables:
#> ..$ Gene : chr [1:109] "BIOHC" "BIOHC" "BIOHC" "BIOH" ...
#> ..$ Species: chr [1:109] "CELJU" "SACD2" "TERTT" "AERHH" ...
#> ..$ Protein: chr [1:109] "B3PI89" "Q21FY5" "C5BMZ8" "A0KF11" ...
#> ..$ family : chr [1:109] "AB hydrolase superfamily. Carboxylesterase BioH family" "AB hydrolase superfamily. Carboxylesterase BioH family" "AB hydrolase superfamily. Carboxylesterase BioH family" "AB hydrolase superfamily. Carboxylesterase BioH family" ...
#> $ AB hydrolase superfamily. Epoxide hydrolase family :'data.frame': 20 obs. of 4 variables:
#> ..$ Gene : chr [1:20] "CEEH1" "CEEH2" "DEH1" "DEHA" ...
#> ..$ Species: chr [1:20] "CAEEL" "CAEEL" "MORSB" "BURSP" ...
#> ..$ Protein: chr [1:20] "G5EBI4" "G5EDL5" "Q01398" "Q1JU72" ...
#> ..$ family : chr [1:20] "AB hydrolase superfamily. Epoxide hydrolase family" "AB hydrolase superfamily. Epoxide hydrolase family" "AB hydrolase superfamily. Epoxide hydrolase family" "AB hydrolase superfamily. Epoxide hydrolase family" ...
#> [list output truncated]
#> NULL
#> [1] "#################### UniProt_ProteinFamily_Human ####################"
#> tibble [14,384 × 5] (S3: tbl_df/tbl/data.frame)
#> $ Gene : chr [1:14384] "IAH1" "PLB1" "PA1B2" "PA1B3" ...
#> $ Protein : chr [1:14384] "Q2TAA2" "Q6P1J6" "P68402" "Q15102" ...
#> $ family : chr [1:14384] "'GDSL' lipolytic enzyme family. IAH1 subfamily" "'GDSL' lipolytic enzyme family. Phospholipase B1 subfamily" "'GDSL' lipolytic enzyme family. Platelet-activating factor acetylhydrolase IB beta/gamma subunits subfamily" "'GDSL' lipolytic enzyme family. Platelet-activating factor acetylhydrolase IB beta/gamma subunits subfamily" ...
#> $ Ensembl.Latest: chr [1:14384] NA NA "ENSG00000168092" NA ...
#> $ Symbol.Latest : chr [1:14384] NA NA "PAFAH1B2" NA ...
#> NULL
#> [1] "#################### UniProt_ProteinFamily_Mouse ####################"
#> tibble [12,499 × 5] (S3: tbl_df/tbl/data.frame)
#> $ Gene : chr [1:12499] "IAH1" "PLB1" "PA1B2" "PA1B3" ...
#> $ Protein : chr [1:12499] "Q9DB29" "Q3TTY0" "Q61206" "Q61205" ...
#> $ family : chr [1:12499] "'GDSL' lipolytic enzyme family. IAH1 subfamily" "'GDSL' lipolytic enzyme family. Phospholipase B1 subfamily" "'GDSL' lipolytic enzyme family. Platelet-activating factor acetylhydrolase IB beta/gamma subunits subfamily" "'GDSL' lipolytic enzyme family. Platelet-activating factor acetylhydrolase IB beta/gamma subunits subfamily" ...
#> $ Ensembl.Added: chr [1:12499] "ENSMUSG00000062054" NA NA NA ...
#> $ Symbol.Added : chr [1:12499] "Iah1" NA NA NA ...
#> NULL
#> [1] "#################### VerSeDa_Mouse_SecretomePrediction ####################"
#> 'data.frame': 23020 obs. of 8 variables:
#> $ Ensembl : chr "ENSMUSG00000000001" "ENSMUSG00000000003" "ENSMUSG00000000028" "ENSMUSG00000000037" ...
#> $ Uniprot : chr "Q9DC51" "O08976, Q3UV89;B1AVU3" "Q9Z1X9, Q3UI99;F8WJ72;D3Z0L5" "B1AVB5;B1AVB4;B1AVB3;B1AVB2;B1AVB1;E9Q796" ...
#> $ SignalP : chr "0.104" "0.783;0.783" "0.134;0.134;0.134" "0.102;0.102;0.102;0.100;0.108;0.102" ...
#> $ TargetP : chr "0.057" "0.967;0.967" "0.245;0.245;0.245" "0.064;0.064;0.064;0.050;0.097;0.064" ...
#> $ TMHMM : chr "PredHel=0" "PredHel=0;PredHel=0" "PredHel=0;PredHel=0;PredHel=0" "PredHel=0;PredHel=0;PredHel=0;PredHel=0;PredHel=0;PredHel=0" ...
#> $ PredGPI : chr "0.504646" "0.274593;0.242442" "0.841856;0.851992;0.667247" "0.713550;0.715782;0.858424;0.784756;0.536397;0.712628" ...
#> $ SecretomeP : chr "0.649" "0.840;0.871" "0.308;0.265;0.848" "0.454;0.544;0.342;0.566;0.573;0.503" ...
#> $ WoLF.PSORT.extr.score: chr "NA" "18;23" "14;13;19" "NA;NA;NA;NA;NA;NA" ...
#> NULL人：tutorials/Prepare-Human-Database.Rmd
小鼠：tutorials/Prepare-Mouse-Database.Rmd
果蝇：tutorials/Prepare-Fly-Database.Rmd
sessionInfo()
#> R version 4.4.3 (2025-02-28 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 26200)
#>
#> Matrix products: default
#>
#>
#> locale:
#> [1] LC_COLLATE=Chinese (Simplified)_China.utf8
#> [2] LC_CTYPE=Chinese (Simplified)_China.utf8
#> [3] LC_MONETARY=Chinese (Simplified)_China.utf8
#> [4] LC_NUMERIC=C
#> [5] LC_TIME=Chinese (Simplified)_China.utf8
#>
#> time zone: Asia/Shanghai
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] BiologyDBLight_0.0.0.9000 badger_0.2.5
#>
#> loaded via a namespace (and not attached):
#> [1] vctrs_0.6.5 cli_3.6.5 knitr_1.51
#> [4] rlang_1.1.6 xfun_0.55 otel_0.2.0
#> [7] generics_0.1.4 S7_0.2.1 jsonlite_2.0.0
#> [10] glue_1.8.0 htmltools_0.5.9 rappdirs_0.3.3
#> [13] scales_1.4.0 rmarkdown_2.30 dlstats_0.1.7
#> [16] grid_4.4.3 tibble_3.3.0 evaluate_1.0.5
#> [19] fastmap_1.2.0 yaml_2.3.12 lifecycle_1.0.4
#> [22] BiocManager_1.30.27 rvcheck_0.2.1 compiler_4.4.3
#> [25] dplyr_1.1.4 fs_1.6.6 RColorBrewer_1.1-3
#> [28] pkgconfig_2.0.3 rstudioapi_0.17.1 farver_2.1.2
#> [31] digest_0.6.39 R6_2.6.1 tidyselect_1.2.1
#> [34] pillar_1.11.1 magrittr_2.0.4 tools_4.4.3
#> [37] gtable_0.3.6 yulab.utils_0.2.3 ggplot2_4.0.1