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: RUNX1

    Description: runt-related transcription factor 1

    Entrez Gene ID: 861

    SwissProt Acc Number: Q01196

    RefSeq: NM_001001890

    It was suspected to be CHD related:

    .."The clinical significance of copy number variants (CNVs) in congenital heart disease (CHD) continues to be a challenge. Furthermore, CNV gene frequency spectra were enriched (P<0.05) for losses at: FKBP6, ELN, GTF2IRD1, GATA4, CRKL, TBX1, ATRX, GPC3, BCOR, ZIC3, FLNA and MID1; and gains at: PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, HRAS, GATA6 and RUNX1."..

    From PMID: 22318994, in Journal Physiol Genomics. , 2012


    References

    There were 1 potential papers with RUNX1 and CHD.

    PMIDTitleJournalsDetails
    22318994 Human gene copy number spectra analysis in congenital heart malformations.Physiological genomicsMore Details

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



    PPI interactions

    There were totally 75 unique genes interacted with RUNX1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CBFB Co-crystal Structure10856244|11742995|14729951|22498736|15331439|10856244,11276260,17431401 No
    AES Two-hybrid10825294 No
    JUN Reconstituted Complex11274169|11274169|11641401 CHD related
    FOS Reconstituted Complex11274169|11274169|11641401 CHD related
    ELF4 Affinity Capture-Western10207087|10207087 No
    ETS1 Reconstituted Complex10207087 CHD related
    ELF2 Reconstituted Complex10207087 No
    EFNA2 Reconstituted Complex10207087 No
    TLE1 Two-hybrid9751710 No
    CBFA2T2 Affinity Capture-Western9447981|22498736 No
    UBC Affinity Capture-Western16046550 No
    HIPK2 Affinity Capture-Western16917507 No
    EP300 Affinity Capture-Western16917507|14752096 CHD related
    KAT6A Affinity Capture-MS11742995|11742995|15331439 No
    TCF12 Affinity Capture-Western15333839 No
    TCF3 Affinity Capture-Western15333839 No
    RUNX1T1 Co-purification10882117|22498736 No
    RUNX1 Affinity Capture-Western18073335 CHD related
    PML Affinity Capture-Western18073335|15331439|15331439 No
    RARA Affinity Capture-Western18073335 No
    HDAC2 Affinity Capture-Western18073335|22498736 CHD related
    SMARCA4 Affinity Capture-Western20506188 No
    SMARCB1 Affinity Capture-Western20506188 No
    SMARCC1 Affinity Capture-Western20506188 No
    MLL Affinity Capture-Western22012064 No
    RBM14 Reconstituted Complex19585539 No
    CBFA2T3 Affinity Capture-MS22498736 No
    PRMT1 Affinity Capture-MS22498736|22498736 No
    CREBBP Affinity Capture-MS15331439 No
    UXT Two-hybrid17635584|17635584|17635584 No
    CTBP2 Two-hybrid17635584 No
    CCND3 in vitro;in vivo;yeast 2-hybrid16287839 No
    AR in vitro10521447 CHD related
    WWTR1 in vitro11118213 No
    CCND2 in vivo16287839 CHD related
    CCND1 in vivo16287839 CHD related
    NCOR2 yeast 2-hybrid16042694 No
    CDK6 in vivo17431401 No
    CEBPA in vivo17431401 No
    SUV39H1 Affinity Capture-Western12917624|12917624|16652147|16652147|12917624 No
    KAT6B Affinity Capture-Western11965546 No
    PAX5 Reconstituted Complex10455134|10455134 No
    YAP1 Two-hybrid10228168|18701449|10228168 No
    SMAD3 Affinity Capture-Western10531362 CHD related
    SMAD1 Affinity Capture-Western10531362 CHD related
    SMAD2 Affinity Capture-Western10531362 CHD related
    SMAD5 Affinity Capture-Western10531362 CHD related
    VDR Reconstituted Complex12460926 CHD related
    CEBPB Reconstituted Complex8622667|8622667 No
    TRAF6 Affinity Capture-Western18768464 No
    FHL2 Affinity Capture-Western18768464 No
    MYOD1 Affinity Capture-Western20195544|20195544 No
    HDAC1 Affinity Capture-Western16652147|21059642 CHD related
    HDAC3 Affinity Capture-Western16652147|21059642 CHD related
    tat Reconstituted Complex19454010 No
    NCOR1 Reconstituted Complex10882117 No
    SIAH1 Affinity Capture-Western18073335 No
    UBE2L6 Reconstituted Complex18073335 No
    SIN3A Affinity Capture-Western14729951 No
    NR4A2 Affinity Capture-Western21468021 CHD related
    TRIM33 Affinity Capture-MS20603019 No
    STUB1 Affinity Capture-Western19524548|19524548 No
    CDK1 Biochemical Activity21059642 CHD related
    TAL1 Affinity Capture-MS19497860 No
    C17orf79 Reconstituted Complex22193545 No
    SPEN Protein-peptide18332109 No
    DNMT1 Affinity Capture-Western15735013|15735013|15735013 No
    ELAVL1 Affinity Capture-RNA19322201 No
    HLA-DMA Affinity Capture-Western22498736 No
    MYST3 in vivo16702405 No
    FOXP3 in vitro;in vivo17377532 CHD related
    HIPK1 in vivo16917507 No
    TAZ in vitro;in vivo11118213 No
    TLE2 in vivo10825294 No
    MYST4 in vivo11965546 No


    Involved FDA drugs

    There was no drug associated with RUNX1