How to Build CHD@ZJU

CHD related Articles were retrieved from Pubmed, by entering keywords "coronary heart disease" and constrict the publish date from 2000/1/1 to now (2013/1/23). As a result, totally 115898 articles were found and their abstracts were downloaded for text mining. Since some articles didn't contain abstracts, only 88396 abstracts remained.

The text-mining process to get CHD related genes could be divided in to 5 following steps:

  • 1) Extracting all keywords from abstracts and ignoring those keywords start with numbers. 101402 keywords were extracted.

  • 2) Input these keywords into Gene library in ArrayTrack and find possible related genes. 4674 genes were then found.

  • 3) Put these 4674 genes again into pubmed abstracts to find related aticles. Only genes which offical name or there keyword description (such as prolactin for gene PRL) could be found in the abstract would be remained. As a result, 1247 genes were remained.

  • 4) Manually examined on the 1247 genes to validate it was acutally related to CHD. Some genes would be filtered if it represents other meanings (such as gene CAD, Entrez ID:790, carbamoyl-phosphate synthetase 2, is mostly meant coronary arterial disease in articles). 681 genes were then validated with at least one reference.

  • 5) All genes was compared with 1078 CHD genes in RGD database, and 370 genes were overlapped. These 370 genes were labels as "RGD_Supported" and the other 293 genes were labels as "REFERED". All 663 genes had supported references in CHD@ZJU which were examined by step 4.
  • How To contact Us

    Collaboration Information: Prof. Xiaohui Fan (fanxh@zju.edu.cn)

    Website using assistance : Leihong Wu (11019004@zju.edu.cn)



    Basic Information

    Gene Name: JAK1

    Description: Janus kinase 1

    Entrez Gene ID: 3716

    SwissProt Acc Number: P23458

    RefSeq: NM_002227

    It was supported literatures to be a novel CHD related gene:

    .."Imidapril and candesartan cilexitil prevented the increase in phosphorylated JAK1 and STAT3, thereby suggesting that angiotensin II, especially angiotensin II type I receptor, partially mediates activation of myocardial JAK-STAT pathway in acute myocardial ischemia."..

    From PMID: 11162135, in Journal J Mol Cell Cardiol. , 2001


    References

    There were 1 potential papers with JAK1 and CHD.

    PMIDTitleJournalsDetails
    11162135 Myocardial ischemia activates the JAK-STAT pathway through angiotensin II signaling in in vivo myocardium of rats.Journal of molecular and cellular cardiologyMore Details

    NOTEs: These result is mostly from TEXT-MINING and there might have mismatches.



    PPI interactions

    There were totally 79 unique genes interacted with JAK1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    STAT3 Reconstituted Complex11751884|11722592|11722592,11940572,11294897,10918587,12244095,11350938,12626508,8626374,12576423,14551213,8272872,9566874 CHD related
    ABL2 Affinity Capture-Western9774693 No
    TEC Affinity Capture-Western9178903 No
    BTK Affinity Capture-Western9178903 No
    IRS1 Biochemical Activity9492017|11162588 CHD related
    IGF1R Reconstituted Complex9492017|9492017 CHD related
    IL2RB Affinity Capture-Western7973659|7973658|7973659,12133952,8700888 No
    IL6ST Affinity Capture-Western11468294|11468294 CHD related
    STAM2 Biochemical Activity10993906 No
    STAT5B Two-hybrid9047382|9047382 No
    STAT5A Two-hybrid9047382|9047382|9047382 No
    IL21R Affinity Capture-Western11016959 No
    GRB2 Affinity Capture-Western11527382|11527382,8536716 CHD related
    IL9R Affinity Capture-Western8756628 No
    TSHR Affinity Capture-Western10809230 No
    RAF1 Affinity Capture-Western9446616 CHD related
    HIST3H3 Biochemical Activity21151131 No
    SOCS1 Affinity Capture-Western10707961 CHD related
    SOCS3 Affinity Capture-Western10707961|10373548|10707961 CHD related
    PLCG2 in vivo14978237 No
    CXCR4 in vivo12163560 CHD related
    PDGFRB in vitro;in vivo8657151,9484840 No
    PDGFRA in vitro11468294 No
    PRKCZ in vitro;in vivo15526032 No
    FES in vivo11160325 No
    IL3RA in vivo15988755 No
    STAT6 in vitro10856136 CHD related
    PLA2G4A in vivo8612580 CHD related
    INPP5D in vivo10875931 No
    SH2B2 in vivo11751854 No
    JAKMIP1 in vitro;in vivo15277531 No
    JAK1 in vitro9597132 CHD related
    STAT1 in vitro;in vivo11722592,7657660,11294897,10918587,15322115,7543024,11839738,12817007,7690989,12637327,10982844 CHD related
    STAT2 in vitro;in vivo9020188 No
    ATIC Affinity Capture-MS17353931 No
    ARRB1 Affinity Capture-MS17353931 No
    ELF3 Affinity Capture-MS17353931 No
    GNB2L1 Affinity Capture-Western12960323|12960323|12960323 No
    IL27RA Affinity Capture-Western12734330 No
    PRMT5 Reconstituted Complex10531356|10531356 No
    SHB Reconstituted Complex12200137|12200137 No
    IL10RA Reconstituted Complex12374810|12133952 CHD related
    PTK2B Affinity Capture-Western10702271|10702271 No
    BRCA1 Affinity Capture-Western11163768 CHD related
    PTPN11 Reconstituted Complex8995399|12403768|8995399,12403768,11036942 CHD related
    TYK2 Affinity Capture-Western7589562 No
    TNFRSF1A Reconstituted Complex9510175|11801527|11801527 CHD related
    IRS2 Affinity Capture-Western7499365|7499365 CHD related
    ELP2 Affinity Capture-Western10954736|10954736|10954736 No
    CSF3R Affinity Capture-Western7512720 No
    IL5RA Affinity Capture-Western9516124|9516124 No
    PTPN6 Biochemical Activity7629131 No
    PLAUR Affinity Capture-Western9417082|9417082 CHD related
    IFNAR2 Reconstituted Complex12133952|16710296|12133952 No
    IL4R Reconstituted Complex12133952|12242343 CHD related
    IFNGR1 Reconstituted Complex12133952|21689637 No
    GHR Affinity Capture-Western10502458|10502458 CHD related
    EIF2C4 Affinity Capture-MS19167051 No
    CSF2RB Affinity Capture-Western21965659 No
    TIRAP Affinity Capture-MS21903422 No
    UBC Affinity Capture-MS21987572|21139048|21890473|21906983|22505724 No
    SIRT1 Affinity Capture-Western22542455 CHD related
    EGFR Affinity Capture-MS18271526 CHD related
    TOP1 Protein-peptide12549820 No
    STAM in vivo9133424 No
    CCR1 in vivo14674010 CHD related
    CCR5 in vivo10037796 CHD related
    IL7R in vivo8647212,15996891 No
    IL2RG in vivo7973658 No
    INSR in vitro;in vivo12456798,9492017 No
    EIF2AK2 in vivo17290288 No
    PTPRC in vitro11201744 CHD related
    MDK in vitro9452495 CHD related
    PIK3R1 in vivo9774657 CHD related
    FER in vitro12738762 No
    SYK in vitro10825200 No
    JAK3 in vitro;in vivo9553136,12559972 No
    OSMR in vivo10586060 No
    PTPN2 in vitro;in vivo11909529,15588985 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB04716"2-(1,1-DIMETHYLETHYL)9-FLUORO-3,6-DIHYDRO-7H-BENZ[H]-IMIDAZ[4,5-F]ISOQUINOLIN-7-ONE"
    experimentalDB08183"3-{(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}-3-oxopropanenitrile"