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: PTPN11

    Description: "protein tyrosine phosphatase, non-receptor type 11"

    Entrez Gene ID: 5781

    SwissProt Acc Number: Q06124

    RefSeq: NM_002834

    It was suspected to be CHD related:

    .."Considering both syndromes share the mutation of PTPN11 gene, coronary arterial involvement could be related to the gene aberration and should be screened even if the patient shows no symptoms of ischemic heart disease."..

    From PMID: 19207402, in Journal Congenit?Heart?Dis.? , 2009


    References

    There were 2 potential papers with PTPN11 and CHD.

    PMIDTitleJournalsDetails
    21060863 "Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo."PLoS geneticsMore Details
    19207402 Coronary artery dilatation in LEOPARD syndrome. A child case and literature review.Congenital heart diseaseMore Details

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



    PPI interactions

    There were totally 139 unique genes interacted with PTPN11. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    STAT5A Reconstituted Complex10617656|10617656|12060651,12237455,10617656 No
    STAT5B Reconstituted Complex10617656|10617656|10617656 No
    CSF3R Far Western9824671|9824671 No
    JAK1 Reconstituted Complex8995399|12403768|8995399,12403768,11036942 CHD related
    JAK2 Reconstituted Complex8995399|7559603,8912646,8995399 CHD related
    SOCS3 Affinity Capture-Western12403768|12403768|10777583|12403768 CHD related
    GAB2 Affinity Capture-Western12135708|11287610,10068651,11812650 No
    IRS1 Reconstituted Complex8505282|9756938|8505282,9756938,7935386 CHD related
    KIT Reconstituted Complex7523381|12444928|7523381,9528781 No
    SELE Affinity Capture-Western11602579|11602579 CHD related
    CAV1 Affinity Capture-Western12176037 CHD related
    CDH5 Affinity Capture-Western10681592 CHD related
    CTNNB1 Affinity Capture-Western10681592 CHD related
    PTK2B Affinity Capture-Western10880513|10880513|10880513 No
    GHR Reconstituted Complex10976913|9632636 CHD related
    PTPN11 Two-hybrid9847309 CHD related
    PAF1 Affinity Capture-Western21726809 No
    CDC73 Affinity Capture-Western21726809 No
    LEO1 Affinity Capture-Western21726809 No
    CTR9 Affinity Capture-Western21726809 No
    RTF1 Affinity Capture-Western21726809 No
    WDR61 Affinity Capture-Western21726809 No
    CSF2RBP1 Affinity Capture-Western9361008 No
    IFNAR1 in vitro;in vivo9029147 No
    PDGFRA in vitro;in vivo8943348 No
    TEK in vitro;in vivo;yeast 2-hybrid10521483 CHD related
    STAT1 in vitro;in vivo12270932 CHD related
    SPRY2 in vitro15031289 No
    HNRNPU in vitro8943344 No
    MVP in vitro15133037,15588985 No
    BDKRB2 in vivo12177051 CHD related
    CAT in vitro15556604 CHD related
    SIRPA in vitro8943344 No
    ARHGAP1 in vitro15169898,15588985 No
    MS4A2 in vitro9379041 No
    PLCG1 in vitro15563458 CHD related
    KIR2DL5A in vitro15187115 No
    RET in vitro12959980 No
    IFNGR1 in vitro10022928 No
    PTPN6 in vivo8541543 No
    NTRK1 in vitro9282923 No
    NTRK2 in vitro10386953 No
    CHUK in vivo11136824 CHD related
    PIK3CG in vivo10386953 CHD related
    MAPK3 in vitro8197172 CHD related
    PILRB in vitro;in vivo10327049,11812650 No
    CTLA4 in vitro;in vivo8638161 CHD related
    BCR in vivo12115002 CHD related
    LIFR in vitro;in vivo10800945 No
    LCK in vitro10617656 No
    KLRC1 in vitro;in vivo9485206 No
    MET in vivo8662733 No
    SYNCRIP Two-hybrid9847309 No
    EGFR Affinity Capture-MS16729043|7673163|9756944 CHD related
    ERBB2 Affinity Capture-MS16729043|9756944|16729043 CHD related
    ERBB4 Affinity Capture-MS16729043 No
    TREML1 Affinity Capture-Western15128762|15128762 No
    BTLA Affinity Capture-Western12796776|12796776 No
    CSF2RB Affinity Capture-Western9162089|9162089 No
    STAT3 Affinity Capture-Western11594781 CHD related
    FRS2 Two-hybrid10650943|10650943|11360177|9632781|9632781 No
    IRS2 Affinity Capture-Western8910607|8910607 CHD related
    GRB2 Affinity Capture-Western10747947|8041791|9824671|8995399|9362449|9632781|10080542|19380743|9361008 CHD related
    ROS1 Two-hybrid11266449 No
    PDGFRB Two-hybrid11266449 No
    INSR Reconstituted Complex8135823|7493946 No
    IL4R Reconstituted Complex11714803 CHD related
    IL6ST Affinity Capture-Western12403768|10946280|9388212|10777583 CHD related
    PLCG2 Affinity Capture-Western12135708 No
    GAB3 Affinity Capture-Western11739737|11739737 No
    IGF1R Affinity Capture-Western10082579|7642582|7642582 CHD related
    PTK2 Affinity Capture-Western10082579|10655584,7589239,8986614,10082579 No
    EPHA2 Affinity Capture-Western10655584|10655584 No
    SLAMF1 Affinity Capture-Western11806999|11689425|11806999 No
    INPP5D Affinity Capture-Western9110989|11157475|9110989 No
    PECAM1 Affinity Capture-Western10801826|10350061|10350061|9774457|9774457|9054388|9054388 CHD related
    GAB1 Affinity Capture-Western11940581|9658397|9804835|9804835 No
    CD33 Affinity Capture-Western10206955|10206955 No
    BCAR1 Affinity Capture-Western9188452 No
    C6orf25 Affinity Capture-Western11544253|11544253 No
    EPOR Affinity Capture-Western8639815 No
    LAIR1 Affinity Capture-Western10903717|9285412|9285412 No
    PILRA Affinity Capture-Western10903717|10660620 No
    FYN Affinity Capture-Western10212213|11157475 No
    Cd244 Affinity Capture-Western11689425 No
    CD84 Affinity Capture-Western11689425 No
    LY9 Affinity Capture-Western11689425 No
    PIK3R1 Affinity Capture-Western9918857|9361008 CHD related
    PRLR Affinity Capture-Western10991949 No
    SLAMF6 Affinity Capture-Western11489943|11489943 No
    SOS1 Affinity Capture-Western9632781 No
    MPZL1 Affinity Capture-Western9792637 No
    SIGLEC11 Affinity Capture-Western11986327|11986327 No
    CRKL Affinity Capture-Western9344843|9344843 No
    LILRB4 Protein-peptide9973385|9422771 No
    FCRL3 Reconstituted Complex12051764 No
    CEACAM1 Affinity Capture-Western9867848 No
    SIT1 Affinity Capture-Western10209036|10209036,11491537,11433379 No
    FCGR2B Affinity Capture-Western10382761 No
    CBL Affinity Capture-Western18519587|17330819|11157475 No
    UBC Affinity Capture-MS21139048|21890473 No
    SOCS1 Affinity Capture-Western14522994 CHD related
    ELAVL1 Affinity Capture-RNA19322201 No
    ERBB3 Affinity Capture-Western9756944 No
    CBLB Affinity Capture-Western17330819 No
    MYC Affinity Capture-Western17157259 CHD related
    CXCR4 Affinity Capture-Western11157475|11157475 CHD related
    LRRK1 Affinity Capture-MS20697350 No
    MAP3K5 Affinity Capture-Western19287004 CHD related
    PIK3R2 Affinity Capture-MS19380743 No
    CRK Affinity Capture-MS19380743 No
    GSK3B Co-fractionation22939629 CHD related
    PPIF Co-fractionation22939629 No
    PRKCA in vivo11781100 CHD related
    PRKCB in vitro;in vivo11781100 CHD related
    TNFRSF1A in vivo11786908 CHD related
    TIE1 in vivo10949653 No
    SHC1 in vitro10650943 No
    LEPR in vivo11018044 CHD related
    PXN in vitro;in vivo10655584,8986614,10082579 No
    DAB1 in vitro15062102 No
    IRS4 in vitro12774026 No
    SIGLEC7 in vitro;in vivo10499918 No
    ACTN4 in vitro;in vivo11382784 No
    PRKCH in vivo11781100 CHD related
    PAG1 in vitro10790433 No
    FRS3 in vitro11432792 No
    NEDD9 in vitro;in vivo8879209 No
    SIGLEC12 in vitro;yeast 2-hybrid11328818 No
    FLT1 yeast 2-hybrid9600074 CHD related
    KDR in vivo9405464 CHD related
    FLT4 in vivo15102829 No
    SRC in vivo14687660 CHD related
    AXL in vivo15507525 No
    GRIN2B in vitro;in vivo10381539 No
    MPL in vivo8541543 No
    MAP3K4 in vivo15601262 No
    CCKBR in vitro;in vivo16963136 No
    DDR1 in vivo;yeast 2-hybrid16337946 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB02779Dodecane-Trimethylamine