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: HMGA1

    Description: high mobility group AT-hook 1

    Entrez Gene ID: 3159

    SwissProt Acc Number: P17096

    RefSeq: NM_002131

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

    ..This report is the first to describe HMGA1 as one of the first mediators in the development of human atherosclerotic plaques...

    From PMID: 15901130, in Journal Pathol Res Pract. , 2005


    References

    There were 1 potential papers with HMGA1 and CHD.

    PMIDTitleJournalsDetails
    23302499 Lack of association of the HMGA1 IVS5-13insC variant with type 2 diabetes in an ethnically diverse hypertensive case control cohort.Journal of translational medicineMore Details

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



    PPI interactions

    There were totally 44 unique genes interacted with HMGA1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SP1 Reconstituted Complex12665574|12665574|20335021|12665574 No
    CEBPB Reconstituted Complex12665574|12665574 No
    ELF1 Reconstituted Complex7862168|7862168 No
    ATF2 Reconstituted Complex10357819|10357819 CHD related
    JUN Reconstituted Complex10357819|10357819 CHD related
    IRF1 Reconstituted Complex10357819|10357819 CHD related
    CHD1 Affinity Capture-Western18817785 No
    NPM1 Far Western16293633 No
    PARP1 Reconstituted Complex16204234 CHD related
    POU2F1 Reconstituted Complex9823775|9823775 No
    POU2F2 Reconstituted Complex9823775|9823775 No
    NFKB1 Reconstituted Complex9809067 CHD related
    RN7SK Protein-RNA21087998 No
    ORC6 Reconstituted Complex18234858 No
    ORC2 Affinity Capture-Western18234858 No
    HDAC2 Co-localization22214847 CHD related
    TERF2 Co-fractionation22939629 No
    SRF in vitro9545312 CHD related
    RARG yeast 2-hybrid10428834 No
    RXRA yeast 2-hybrid10428836 CHD related
    EWSR1 Two-hybrid16189514|16189514 No
    NFYA Far Western9388234 No
    POU3F1 Reconstituted Complex7791781|7791781 No
    BANF1 Affinity Capture-MS19759913 No
    PRMT6 Biochemical Activity16293633|16157300|16293633 No
    PPARG Reconstituted Complex18310298|10428834 CHD related
    PRKCA Biochemical Activity10889043 CHD related
    RARA Two-hybrid10428834|10428834 No
    CREBBP Two-hybrid10428834|9809067 No
    KAT2B Biochemical Activity9809067 No
    TP53 Affinity Capture-Western20335021 CHD related
    Stag2 Affinity Capture-MS20360068 No
    KIAA0101 Affinity Capture-MS21628590 No
    UBC Affinity Capture-MS21139048|21906983|22505724 No
    HHV8GK18_gp81 Far Western22379092 No
    HDAC7 Negative Genetic22318606 No
    CBX7 Affinity Capture-Western22214847|22214847 No
    CDK2 Affinity Capture-MS21319273 No
    RNF4 in vitro;yeast 2-hybrid10713105 No
    HIPK2 in vitro;in vivo;yeast 2-hybrid11593421 No
    SUFU yeast 2-hybrid14611647 No
    CSNK2A1 in vitro11034995,2806554 CHD related
    CSNK2A2 in vitro11034995,2806554 No
    CDK1 in vitro;in vivo1939057 CHD related


    Involved FDA drugs

    There was no drug associated with HMGA1