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: HIF1A

    Description: "hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)"

    Entrez Gene ID: 3091

    SwissProt Acc Number: Q16665

    RefSeq: NM_001530

    It was suspected to be CHD related:

    ..Polymorphisms in HIF1A were associated with development of stable exertional angina rather than acute MI as the initial clinical presentation of CAD...

    From PMID: 18035072, in Journal Am Heart J , 2007


    References

    There were 1 potential papers with HIF1A and CHD.

    PMIDTitleJournalsDetails
    18035072 Polymorphisms in hypoxia inducible factor 1 and the initial clinical presentation of coronary disease.American heart journalMore Details

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



    PPI interactions

    There were totally 102 unique genes interacted with HIF1A. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SSX4 Two-hybrid16189514 No
    ZNF197 Affinity Capture-Western12682018 No
    TP53 Affinity Capture-Western12606552|12124396|9537326|12124396,9537326 CHD related
    CREBBP Two-hybrid10202154|10202154|15154850|10202154,17382325,11959977,16543236 No
    PSMA7 Reconstituted Complex11389899 No
    NCOA1 Reconstituted Complex10594042|10594042 No
    STAT3 Affinity Capture-Western18985005 CHD related
    UBC Affinity Capture-Western18694926|18305400|17973296|17875644|17558023|17403672|16611863|16424018|15776016|15382039|21658608|17965024|17237281|21332579|20407014|19738058|19940151|21964756|21124777|22286099|18838541|20668552 No
    NR4A1 Affinity Capture-Western18305400|18305400 CHD related
    SAT1 Reconstituted Complex17875644 No
    GNB2L1 Reconstituted Complex17875644|17244529|17244529 No
    MTA1 Affinity Capture-Western16511565|16511565|16511565 No
    SAT2 Reconstituted Complex17558023 No
    TCEB1 Affinity Capture-Western17558023|21658608|17965024|19940151|17244529 No
    CUL2 Affinity Capture-Western17439941|17132228|19940151 No
    HSPA4 Affinity Capture-Western16507982|16951198|14726529|14726529|19802386|19940151|19940151|19940151|21124777|15319539 No
    SEPT9 Affinity Capture-Western16424018 No
    EGLN1 Reconstituted Complex16407130|15721254|18264140|20724477|15474027,16511565,15721254 CHD related
    BANP Affinity Capture-MS20562859 No
    HDAC4 Affinity Capture-Western19071119 CHD related
    HDAC5 Affinity Capture-Western19071119 No
    USP20 Affinity Capture-Western15776016 No
    OS9 Two-hybrid15721254|15721254 No
    EGLN3 Reconstituted Complex15721254|18264140|15474027,16511565,15721254 CHD related
    SUMO1 Affinity Capture-Western15465032 No
    VHLL Reconstituted Complex14757845 No
    EGLN2 Reconstituted Complex18264140 CHD related
    SMARCA2 Co-localization15347669 No
    SMARCA4 Co-localization15347669 No
    RUVBL2 Affinity Capture-Western20603076 No
    MCM3 Affinity Capture-Western21658608 No
    HSP90AB1 Affinity Capture-Western19802386|20668552 CHD related
    COMMD1 Affinity Capture-Western19802386 No
    STUB1 Affinity Capture-MS19940151|19940151|19940151 No
    TCEB2 Affinity Capture-MS19940151 No
    FBXW7 Affinity Capture-Western21964756 No
    KDM3A Affinity Capture-Western22645302 No
    BCR Affinity Capture-Western21124777 CHD related
    DNAJB1 Affinity Capture-Western21124777 No
    PTGES3 Affinity Capture-Western15319539 No
    NEDD8 Affinity Capture-Western21193393 No
    F12 Affinity Capture-Western18838541 CHD related
    RUNX2 Affinity Capture-Western22351759|22351759 No
    LAMP2 Affinity Capture-Western19458911 CHD related
    PGK1 in vivo8089148 No
    MAPK3 in vitro;in vivo10551817 CHD related
    PER1 in vitro;in vivo11726537 No
    AR in vivo17426252 CHD related
    VHL Affinity Capture-Western14556007|10944113|12004076|11504942|18985005|18305400|17981124|17558023|17558023|17047048|16278378|15805242|12050673|12050673|14691445|12925778|12808024|12606543|12538644|12464182|11566883|11566883|11331613|11292861|11292861|10973499|10973499|10878807|10823831|10823831|20049704|15060148|21358672|11292862|11292862|12086861|15611064|17339318|17339318|11024059|11358837|17986458|11986208|10353251|12351678 No
    PSMC3 Affinity Capture-Western14556007 No
    MDM2 Reconstituted Complex12606552|10640274 CHD related
    HIF1AN Affinity Capture-Western11641274|11641274|19696166|11641274,14734545,17382325 No
    HDAC1 Reconstituted Complex11641274|17273746|17273746|22318606|21148070 CHD related
    HDAC2 Reconstituted Complex11641274 CHD related
    HDAC3 Reconstituted Complex11641274|17273746|17273746|22318606 CHD related
    EP300 Affinity Capture-Western11823643|11959990|15154850|21148070|19696166|15261140 CHD related
    DAP3 Reconstituted Complex10903152 No
    APEX1 Reconstituted Complex10594042 CHD related
    JUN Affinity Capture-Western11739718|19738058 CHD related
    ARNT Affinity Capture-Western11782478|9079689|9079689|20049704 No
    HSP90AA1 Reconstituted Complex9079689|17237281|20724477|21413014|15319539|20668552 CHD related
    Mapk1 Biochemical Activity10551817 No
    Per1 Affinity Capture-Western11726537 No
    ARNTL Two-hybrid9576906|9576906 No
    NAA10 Affinity Capture-Western16511565|16288748|12464182,16288748,16511565 No
    HDAC6 Affinity Capture-Western16951198 No
    SHC1 Affinity Capture-Western12114320 No
    PARP1 Affinity Capture-Western18314489 CHD related
    MYC Affinity Capture-Western15071503 CHD related
    MAX Affinity Capture-Western17418410 No
    MCM7 Affinity Capture-Western21658608 No
    NSFL1C Affinity Capture-Western18775313 No
    FAF2 Affinity Capture-Western18775313 No
    FAF1 Affinity Capture-Western18775313 No
    UBXN7 Affinity Capture-Western18775313|22537386 No
    UBXN1 Affinity Capture-Western18775313 No
    VCP Affinity Capture-Western18775313 No
    SUMO2 Affinity Capture-Western20026589 No
    SP1 Affinity Capture-Western17024177|17024177 No
    RAD23B Affinity Capture-Western22537386 No
    HDAC9 Negative Genetic22318606 No
    RWDD3 Affinity Capture-Western17956732|17956732 No
    USP19 Two-hybrid22128162 No
    UBE2D1 Biochemical Activity15611064 No
    CDC34 Biochemical Activity15611064 No
    COPS5 Affinity Capture-Western15082527|11707426 No
    HDAC7 Affinity Capture-Western21148070 No
    KAT2B Affinity Capture-Western21148070 No
    BHLHE41 Affinity Capture-Western22801492 No
    BRCA1 Affinity Capture-Western16543242 CHD related
    CAPN1 Affinity Capture-Western19458911 No
    BCL2 Affinity Capture-Western20668552 CHD related
    NDN Affinity Capture-Western15978586|15978586 No
    NCOA2 in vitro10594042 No
    HIF3A in vivo11734856 No
    ARNT2 yeast 2-hybrid8927054 No
    CDKN2A in vivo11382768 CHD related
    NAA11 in vivo16638120 No
    CSNK2A1 in vitro17382325 CHD related
    CITED2 in vitro12778114 No
    TSGA10 in vitro;in vivo;yeast 2-hybrid16777103 No
    CTNNB1 in vitro;in vivo17220880 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB08687N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE