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: IGF1R

    Description: insulin-like growth factor 1 receptor

    Entrez Gene ID: 3480

    SwissProt Acc Number: P08069

    RefSeq: NM_000875

    It was suspected to be CHD related:

    ..TRAIL may play an important role in atherosclerosis by regulating IGF1R expression in VSMC in an NF-kappaB-dependent manner...

    From PMID: 18178561, in Journal J Biol Chem , 2008


    References

    There were 2 potential papers with IGF1R and CHD.

    PMIDTitleJournalsDetails
    23832067 Pharmacogenomics of anti-platelet therapy focused on peripheral blood cells of coronary arterial disease patients.Clinica chimica acta; international journal of clinical chemistryMore Details
    18178561 TRAIL stimulates proliferation of vascular smooth muscle cells via activation of NF-kappaB and induction of insulin-like growth factor-1 receptor.The Journal of biological chemistryMore Details

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



    PPI interactions

    There were totally 66 unique genes interacted with IGF1R. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    IRS1 Two-hybrid7559507|8776723|10082579|7559507,8662806,15629149,12220227,8530377 CHD related
    NEDD4 Affinity Capture-Western12697834|19165858 No
    IGF1 Reconstituted Complex1852007 CHD related
    SNAP29 Affinity Capture-Western11423532 No
    ARHGEF12 Two-hybrid11724822|11724822|11724822 No
    PIK3R3 Reconstituted Complex9415396 No
    SHC1 Two-hybrid8776723|16113100|7559507 No
    ESR1 Affinity Capture-Western16113100 CHD related
    PTK2 Affinity Capture-Western10082579 No
    PXN Affinity Capture-Western10082579 No
    PTPN11 Affinity Capture-Western10082579|7642582|7642582 CHD related
    RASA1 Affinity Capture-Western7642582|7642582|7642582 No
    PTPN1 Affinity Capture-Western8999839 CHD related
    GNB2L1 Affinity Capture-Western11884618|20871634 No
    UBC Affinity Capture-Western18632619|17406664|16619240|12821780|17307140|19165858|18632619 No
    EEA1 Affinity Capture-Western18632619|18632619 No
    Arrb1 Affinity Capture-Western12167719 No
    ERBB2 Affinity Capture-Western17307140 CHD related
    CAMP Reconstituted Complex21685939|21685939 No
    SUMO1 Affinity Capture-Western20596523 No
    ARRB2 Affinity Capture-Western19165858|15878855 No
    TP53 Affinity Capture-Western19165858 CHD related
    APP Reconstituted Complex21832049 No
    RUVBL1 Co-fractionation22939629 No
    PRKCD in vivo11884618 CHD related
    PRKD1 in vivo11884618 No
    PIK3R2 in vitro7541045 No
    INSR in vitro7895674 No
    JAK2 in vitro10747872,9492017 CHD related
    MAP3K5 in vitro;in vivo12556535 CHD related
    IRS4 in vitro;in vivo11316748,9553137 No
    DOK4 in vitro12730241 No
    CAV1 in vivo18632619 CHD related
    GNAI2 in vivo11120746 No
    IGF1R in vitro12138114,11591350 CHD related
    CRK in vitro;in vivo;yeast 2-hybrid15522217,12198159,11956190,9642287,8875975,9480911 No
    CSK Two-hybrid10026153 No
    YWHAE Two-hybrid9111084|9111084|9111084 No
    SOCS1 Two-hybrid9727029|9727029 CHD related
    YWHAG Affinity Capture-MS17353931|15324660|15324660 No
    GRB10 Affinity Capture-Western12697834|9506989|8621530,8764099,9506989 No
    EHD1 Reconstituted Complex11423532 No
    IGFBP3 Co-purification9389554 CHD related
    JAK1 Reconstituted Complex9492017|9492017 CHD related
    EGFR Affinity Capture-Western17047074|17307140 CHD related
    YWHAB Reconstituted Complex9581554|9581554,14651979 No
    VAV3 Affinity Capture-Western11094073|11094073 No
    SOCS2 Two-hybrid9727029|9727029|9727029|9727029 No
    GNAI1 Affinity Capture-Western10644671 CHD related
    SOCS3 Reconstituted Complex11071852|11071852|11071852 CHD related
    MDM2 Biochemical Activity18632619|12821780 CHD related
    CBL Biochemical Activity18632619 No
    ARRB1 Affinity Capture-Western15878855 No
    STAT3 in vitro;in vivo11463827 CHD related
    ITGB1 in vitro14522909,11884618 CHD related
    KL in vivo18762812 CHD related
    IGF2 in vivo9972281 CHD related
    PIK3R1 in vitro8697095 CHD related
    INS in vivo1851182 CHD related
    SRC in vitro;in vivo8940173 CHD related
    IRS2 in vivo;yeast 2-hybrid9852124,8662806 CHD related
    YWHAZ in vitro9581554 No
    CRKL yeast 2-hybrid15522217 No
    GIPC1 in vitro;in vivo;yeast 2-hybrid11445579 No
    DOK5 in vivo12730241 No
    KRT27 in vitro15629149 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00030Insulin recombinantFor treatment of Type I and II diabetes mellitus.A10AB01;A10AE05;A10AB04;A10AE04;A10AD05;A10AC03;A10AC01;A10AB05;A10AB03
    approvedDB00046Insulin LisproFor the treatment of Type 1 or 2 diabetes mellitus. To be used in conjunction with an intermediate or long-acting insulin except when used in a continuous insulin infusion pump. A10AB04;A10AC04;A10AD04
    approvedDB00047Insulin GlargineFor the treatment of Type 1 or 2 diabetes mellitus in patients over 17 years old who require a long-acting (basal) insulin for the control of hyperglycemia. May be used in pediatric patients with Type 1 diabetes mellitus who require a long-acting (basal) insulin for glycemic control. A10AE04
    approvedDB00071"Insulin, porcine"For the treatment of type I and II diabetes mellitus.
    approvedDB01277Mecasermin"For the long-term treatment of growth failure in pediatric patients with Primary IGFD or with GH gene deletion who have developed neutralizing antibodies to GH. It is not indicated to treat Secondary IGFD resulting from GH deficiency, malnutrition, hypothyroidism or other causes; it is not a substitute for GH therapy."H01AC03
    experimentalDB02944Alpha-D-Mannose
    experimentalDB04395Phosphoaminophosphonic Acid-Adenylate Ester
    experimentalDB07156"(4Z)-6-bromo-4-({[4-(pyrrolidin-1-ylmethyl)phenyl]amino}methylidene)isoquinoline-1,3(2H,4H)-dione"
    experimentalDB074743-[5-(1H-IMIDAZOL-1-YL)-7-METHYL-1H-BENZIMIDAZOL-2-YL]-4-[(PYRIDIN-2-YLMETHYL)AMINO]PYRIDIN-2(1H)-ONE