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: PKD1

    Description: polycystic kidney disease 1 (autosomal dominant)

    Entrez Gene ID: 5310

    SwissProt Acc Number: P98161

    RefSeq: NM_000296

    It was suspected to be CHD related:

    ..These data suggest that PKD1 contributes to the antiproliferative effect of amlodipine on hCASMCs via JAK/STAT signaling and p21((Waf1/Cip1)) up-regulation...

    From PMID: 18298949, in Journal Biochem Biophys Res Commun.? , 2008


    References

    There were 2 potential papers with PKD1 and CHD.

    PMIDTitleJournalsDetails
    18298949 Amlodipine inhibits cell proliferation via PKD1-related pathway.Biochemical and biophysical research communicationsMore Details
    18505769 Serial analysis of the vascular endothelial transcriptome under static and shear stress conditions.Physiological genomicsMore Details

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



    PPI interactions

    There were totally 27 unique genes interacted with PKD1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PKD2 Two-hybrid9192675|9192675|9192675 No
    RGS7 Two-hybrid10339594|10339594|10339594 No
    FN1 Reconstituted Complex11752017|11752017 CHD related
    COL1A1 Reconstituted Complex11752017 CHD related
    KRT18 Reconstituted Complex11581269|11581269 No
    COL2A1 Reconstituted Complex11406351|11406351 No
    SIAH1 Two-hybrid15284290|15284290|15284290 No
    UBC Affinity Capture-Western15284290 No
    MARK2 Biochemical Activity19011111 No
    JUP in vitro;in vivo11274246 CHD related
    TLN1 in vitro;in vivo11113628 No
    SRC in vitro;in vivo11113628 CHD related
    CDH1 in vitro;in vivo11274246 No
    VIM in vitro;in vivo;yeast 2-hybrid11581269 CHD related
    VCL in vitro;in vivo11113628 CHD related
    ACTN1 in vitro;in vivo11113628 No
    PTK2 in vitro;in vivo11113628 No
    CTNNA1 in vitro;in vivo11274246 CHD related
    CTNNB1 in vitro;in vivo11274246 CHD related
    JAK2 in vitro12007403 CHD related
    DES in vitro;in vivo;yeast 2-hybrid11581269 No
    KRT8 in vitro;in vivo;yeast 2-hybrid11581269 No
    ATF7IP yeast 2-hybrid15231748 No
    HDAC9 Reconstituted Complex15738054|15623513|15623513 No
    Mapk13 Biochemical Activity19135240|19135240 No
    PXN in vitro;in vivo11113628 No
    BCAR1 in vitro;in vivo11113628 No


    Involved FDA drugs

    There was no drug associated with PKD1