Herwig, R. et al.. Analyzing and interpreting genome data at the network level with ConsensusPathDB. (2016) Nature Protocols 11, 1889-1907.Kamburov, A. et al. (2013) The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res.Kamburov, A. et al. (2011) ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Res.Kamburov, A. et al. (2009) ConsensusPathDB--a database for integrating human interaction networks. Nucleic Acids Res.Pentchev, K. et al. (2010) Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinformatics
目前已经更新到 Release 35 (05.06.2021) ,暂时只支持 human yeast mouse 这3个物种。
支持下载全部的五千多基因集
作者整理好的基因集,里面的基因有多种id,包括:
Entrez
Ensembl
symbol (HGNC symbol)
HGNC ID
RefSeq
Unigene
Uniprot
我这里一般是选择symbol (HGNC symbol),如下所示:
Butanoate metabolism - Homo sapiens (human) path:hsa00650 KEGG ACADS,ABAT,AACS,GAD1,GAD2,ACSM1,EHHADH,ACSM3,HADHA,ACSM5,ACSM4,ACSM6,ACAT1,ACAT2,HMGCLL1,HMGCS1,HMGCS2,HMGCL,ACSM2A,ACSM2B,BDH2,BDH1,HADH,L2HGDH,ECHS1,OXCT1,OXCT2,ALDH5A1 Steroid hormone biosynthesis - Homo sapiens (human) path:hsa00140 KEGG HSD17B12,HSD17B1,CYP11B2,HSD11B1L,UGT2A3,UGT2A2,UGT2A1,CYP17A1,UGT1A8,UGT1A9,UGT1A4,UGT1A5,UGT1A6,UGT1A7,UGT1A1,AKR1C2,UGT1A3,CYP7B1,CYP11A1,CYP1B1,UGT1A10,AKR1C4,CYP3A7-CYP3A51P,HSD17B8,UGT2B15,UGT2B17,UGT2B10,UGT2B11,CYP21A2,SRD5A3,SRD5A2,SRD5A1,AKR1C3,HSD11B2,HSD17B6,HSD17B7,UGT2B7,UGT2B4,AKR1C1,HSD3B2,DHRS11,LRTOMT,COMT,STS,SULT1E1,CYP3A7,CYP3A4,CYP3A5,HSD17B2,CYP1A1,CYP1A2,HSD17B3,CYP19A1,AKR1D1,CYP2E1,HSD3B1,SULT2B1,UGT2B28,CYP11B1,HSD11B1,CYP7A1 Cell cycle - Homo sapiens (human) path:hsa04110 KEGG BUB1B,PLK1,PKMYT1,GADD45A,GADD45B,ANAPC11,ANAPC10,ANAPC13,GADD45G,ESPL1,WEE2,WEE1,CUL1,CDKN2B,CDKN2C,CDKN2A,CDKN2D,MDM2,PRKDC,CCND1,CCND3,CCND2,GSK3B,SFN,DBF4,RBX1,CCNH,FZR1,CDKN1C,CDKN1B,CDKN1A,CDC16,CCNE2,CCNE1,TTK,STAG2,CHEK2,CHEK1,SMC1A,SMC1B,BUB1,BUB3,CDC25C,CDC25B,CDC25A,STAG1,ANAPC1,ZBTB17,ANAPC2,ANAPC5,ANAPC4,ANAPC7,TP53,CDC27,CDC26,CDC23,CDC14B,CDC14A,CDC20,TFDP2,TFDP1,HDAC1,HDAC2,SMAD4,ATM,SMAD2,SMAD3,MAD2L1,ATR,ABL1,CDC6,CDC7,SKP2,SKP1,SMC3,PTTG1,PTTG2,RBL1,RBL2,E2F5,EP300,MYC,CDK1,CDK2,CDK4,CDK6,CDK7,CDC45,MAD2L2,TGFB1,TGFB2,TGFB3,YWHAZ,CCNA2,CCNA1,MAD1L1,YWHAQ,RB1,YWHAH,YWHAB,YWHAG,YWHAE,PCNA,RAD21,ORC6,ORC4,ORC5,ORC2,ORC3,ORC1,MCM7,MCM6,MCM5,MCM4,MCM3,MCM2,CCNB3,CCNB2,CCNB1,E2F4,E2F3,E2F2,E2F1,CREBBP
其次,它提供一个Cytoscape的插件, With the ConsensusPathDB plugin for Cytoscape you can mine evidence (publications, detection methods, pathways, etc.) for interactions loaded in Cytoscape and highlight interactions that have not been detected previously. Please read our paper on the plugin to learn how to use it.
We thank Dr.Jianming Zeng(University of Macau), and all the members of his bioinformatics team, biotrainee, for generously sharing their experience and codes.