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: E2F1

    Description: E2F transcription factor 1

    Entrez Gene ID: 1869

    SwissProt Acc Number: Q01094

    RefSeq: NM_005225

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

    ..Hammerhead ribozymes targeted against cyclin E and E2F1 cooperate to down-regulate coronary smooth muscle cell proliferation...

    From PMID: 15772936, in Journal J Gene Med. , 2005


    References

    There were 1 potential papers with E2F1 and CHD.

    PMIDTitleJournalsDetails
    15772936 Hammerhead ribozymes targeted against cyclin E and E2F1 cooperate to down-regulate coronary smooth muscle cell proliferation.The journal of gene medicineMore Details

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



    PPI interactions

    There were totally 98 unique genes interacted with E2F1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    NCOA6 Two-hybrid14638867|14638867|14638867 No
    PKIB Two-hybrid12748276 No
    CREBBP Two-hybrid12748276|8932363 No
    TEAD3 Two-hybrid12748276 No
    MYBL2 Two-hybrid12748276 No
    SPIB Two-hybrid12748276 No
    MGA Two-hybrid12748276 No
    TRRAP Affinity Capture-Western9708738|11418595 No
    HDAC1 Affinity Capture-Western10734134 CHD related
    RBBP4 Affinity Capture-Western10734134 No
    TP53BP1 Reconstituted Complex8896460|8896460 No
    MDM4 Two-hybrid12532331|12532331 CHD related
    SP1 Affinity Capture-Western8657142|8657142|10547281|10547281|8657141|10547281,10850422 No
    RNF144A Two-hybrid12411495 No
    FHL2 Two-hybrid12411495 No
    CDK2 Reconstituted Complex7969176 No
    CCNA2 Affinity Capture-Western7969176|7969176|12501191 CHD related
    SP2 Affinity Capture-Western10547281|10547281 No
    SP4 Affinity Capture-Western10547281|10547281 No
    SP3 Affinity Capture-Western10547281|10547281 No
    NFKB1 Reconstituted Complex9368006|9368006 CHD related
    ARID3A Reconstituted Complex9780002|9780002 No
    CCNA1 Reconstituted Complex10022926|16774918 No
    TFDP2 Reconstituted Complex7739537 No
    CDK7 Affinity Capture-Western10428966 No
    GSK3B Affinity Capture-Western18367454|18367454 CHD related
    UBC Affinity Capture-Western18367454|16170383|15494392|11245432|16924238|22580462|23001041 No
    TBP Affinity Capture-Western17111193 No
    YWHAQ Two-hybrid15494392|15494392 No
    E2F4 Co-localization16357170 No
    CDKN1A Co-localization15964998 CHD related
    KAT2A Affinity Capture-Western11418595 No
    KAT5 Affinity Capture-Western15121871 No
    ASH2L Affinity Capture-Western17612494 No
    NRIP1 Affinity Capture-Western20410059|20410059 No
    ATAD2 Affinity Capture-Western20855524|20855524 No
    CSNK1A1 Affinity Capture-Western19759023 No
    IGF1 Two-hybrid14681231 CHD related
    FZR1 Affinity Capture-Western22580462 No
    ANAPC5 Affinity Capture-Western22580462 No
    ESR1 Affinity Capture-Western22216287 CHD related
    DDB1 Affinity Capture-MS9418871 No
    DDB2 Affinity Capture-MS9418871|9418871 No
    XIAP Affinity Capture-Western21653699 CHD related
    BIRC3 Affinity Capture-Western21653699 No
    CEBPD Affinity Capture-Western15674331 No
    CDK3 in vivo11733001,8846921 No
    NDN Two-hybrid9422723|14593116|9422723|14593116,9422723 No
    TOPBP1 Affinity Capture-Western12697828|14576433|12697828|17006541|12697828,14576432,17006541 No
    PHB Reconstituted Complex14637159|14637159|14500729|12065415|10523633|15141164 No
    NDNL2 Affinity Capture-Western14593116 No
    RB1 Affinity Capture-Western11470869|12397079|8896460|10869426|7739537|9422723|12963846|16766265|15670817|18216119|15837424|10499802|20871633|11090181|15485814|22768064|17380128|16249186|8657117|1388726,11583618,9125176,16374512 CHD related
    DNMT1 Co-fractionation10888886 No
    RING1 Affinity Capture-Western11583618 No
    NPDC1 Reconstituted Complex11042687|11042687|9181131,11042687 No
    RBL1 Affinity Capture-Western8230483|8657117 No
    TFDP1 Two-hybrid7892279|22629304|9199321 No
    SKP2 Affinity Capture-Western10559858|12097298|17471231|10559858 No
    CUL1 Affinity Capture-Western10559858|11245432|10559858 No
    GTF2H1 Biochemical Activity10428966|10428966 No
    BRD2 Co-purification10965846|17111193|10965846 No
    PURA Reconstituted Complex10597240|10597240 No
    CDT1 Affinity Capture-Western18162579 No
    SIRT1 Affinity Capture-Western19188449 CHD related
    KAT2B Affinity Capture-Western19188449 No
    MDM2 Affinity Capture-Western16170383|18754770|18754770 CHD related
    MCPH1 Affinity Capture-Western18660752|23001041 No
    KLF6 Affinity Capture-Western18521079 No
    LEF1 Affinity Capture-Western17980157 No
    TRIM28 Affinity Capture-Western17704056|22496453 No
    RBX1 Biochemical Activity11245432 No
    HCFC1 Affinity Capture-Western17612494|17612494 No
    KDM1A Biochemical Activity20603083|21320024 No
    SETD7 Biochemical Activity20603083|21320024|22836579 No
    PRDM2 Reconstituted Complex9223517 No
    ATM Biochemical Activity11459832|11459832 No
    ATR Biochemical Activity11459832|11459832 No
    TRIM16 Affinity Capture-Western20729920 No
    NCOA3 Co-localization16648476|15169882 No
    AR Affinity Capture-Western22508987 CHD related
    HDAC2 Negative Genetic22318606 CHD related
    HDAC3 Negative Genetic22318606 CHD related
    HDAC8 Negative Genetic22318606 No
    BRCA1 Affinity Capture-Western21880590 CHD related
    NEDD8 Affinity Capture-Western22836579 No
    SUMO1 Affinity Capture-Western15876874 No
    BIRC2 Affinity Capture-Western21653699 No
    SENP8 Biochemical Activity23001041 No
    CDK1 Biochemical Activity9199321|8087847 CHD related
    TP53 in vitro;in vivo11739724 CHD related
    MNAT1 in vitro10428966 No
    E2F6 in vitro9689056 No
    CHEK2 in vitro;in vivo12717439 No
    CTDP1 in vitro14576433 CHD related
    SERTAD2 in vitro11331592 No
    CEBPE in vitro;in vivo12947005 No
    CDKN2A in vitro11314038 CHD related
    PARP1 in vitro;in vivo14627987 CHD related


    Involved FDA drugs

    There was no drug associated with E2F1