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: PIK3CG

    Description: "phosphoinositide-3-kinase, catalytic, gamma polypeptide"

    Entrez Gene ID: 5294

    SwissProt Acc Number: P48736

    RefSeq: NM_002649

    It was suspected to be CHD related:

    ..We demonstrated that the C- and G-alleles differentially bind the transcription factor EVI1 affecting PIK3CG gene expression in platelets and macrophages. A protein-protein interaction network including up- and down-regulated genes in Pik3cg knockout mice indicated that PIK3CG is associated with gene pathways with an established role in platelet membrane biogenesis and thrombus formation...

    From PMID: 21738486, in Journal PLoS Genet , 2011


    References

    There were 1 potential papers with PIK3CG and CHD.

    PMIDTitleJournalsDetails
    21738486 Maps of open chromatin guide the functional follow-up of genome-wide association signals: application to hematological traits.PLoS geneticsMore Details

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



    PPI interactions

    There were totally 29 unique genes interacted with PIK3CG. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    KRAS Reconstituted Complex10542052|10542052|10542052 No
    UTRN Affinity Capture-MS20562859 No
    PRMT7 Affinity Capture-MS20562859 No
    ZNF282 Two-hybrid21900206 No
    SET Biochemical Activity21419339 No
    NOTCH1 in vivo14583609 CHD related
    ADRBK1 in vivo12163475 CHD related
    IL6ST in vivo10579793 CHD related
    GAB1 yeast 2-hybrid10871282 No
    TPM2 in vitro;in vivo16094730 No
    GSN in vitro;in vivo11577104 No
    BCR Two-hybrid9747873|7606002 CHD related
    ERAS Affinity Capture-Western12774123 No
    PIK3CD Reconstituted Complex9113989|9113989 No
    EPHA8 Affinity Capture-Western11416136 No
    LYN Affinity Capture-Western10318860|7721825|7721825 No
    PIK3R5 FRET12507995|12507995|12507995|12507995|12507995,10488142 No
    NRAS Reconstituted Complex11136978 No
    HRAS Co-crystal Structure11136978 No
    USP45 Affinity Capture-MS19615732 No
    GABARAPL1 Affinity Capture-MS20562859 No
    PRKAA2 Affinity Capture-MS20562859 CHD related
    SYK Affinity Capture-Western7721825 No
    SMPD2 in vivo11238738 No
    SEC14L2 in vitro12757856 No
    CD28 in vivo9915850 CHD related
    GRB2 in vivo10386953 CHD related
    KIT in vitro;in vivo7520444 No
    PTPN11 in vivo10386953 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB02010Staurosporine
    experimentalDB02375Myricetin
    experimentalDB026562-(4-Morpholinyl)-8-Phenyl-4h-1-Benzopyran-4-One
    experimentalDB04216Quercetin
    experimentalDB04769"5-QUINOXALIN-6-YLMETHYLENE-THIAZOLIDINE-2,4-DIONE"
    experimentalDB068312-((9H-PURIN-6-YLTHIO)METHYL)-5-CHLORO-3-(2-METHOXYPHENYL)QUINAZOLIN-4(3H)-ONE
    experimentalDB06836N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE
    experimentalDB07073"5,5-dimethyl-2-morpholin-4-yl-5,6-dihydro-1,3-benzothiazol-7(4H)-one"
    experimentalDB07335"3-[4-AMINO-1-(1-METHYLETHYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-3-YL]PHENOL"
    experimentalDB07503"(5E)-5-[(2,2-DIFLUORO-1,3-BENZODIOXOL-5-YL)METHYLENE]-1,3-THIAZOLIDINE-2,4-DIONE"
    experimentalDB08059"(1S,6BR,9AS,11R,11BR)-9A,11B-DIMETHYL-1-[(METHYLOXY)METHYL]-3,6,9-TRIOXO-1,6,6B,7,8,9,9A,10,11,11B-DECAHYDRO-3H-FURO[4,3,2-DE]INDENO[4,5-H][2]BENZOPYRAN-11-YL ACETATE"
    experimentalDB08300"1-methyl-3-naphthalen-2-yl-1H-pyrazolo[3,4-d]pyrimidin-4-amine"