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: KDR

    Description: kinase insert domain receptor (a type III receptor tyrosine kinase)

    Entrez Gene ID: 3791

    SwissProt Acc Number: P35968

    RefSeq: NM_002253

    It was suspected to be CHD related:

    ..Polymorphisms of?KDR?gene are associated with?coronary heart disease..

    From PMID: 17707181, in Journal J Am Coll Cardiol.? , 2007


    References

    There were 22 potential papers with KDR and CHD.

    PMIDTitleJournalsDetails
    23182004 Reduced number and impaired function of circulating endothelial progenitor cells in patients with abdominal aortic aneurysm.International journal of cardiologyMore Details
    23062532 Role of circulating osteogenic progenitor cells in calcific aortic stenosis.Journal of the American College of CardiologyMore Details
    22344734 Single-nucleotide polymorphisms in the KDR gene in pregnancies complicated by gestational hypertensive disorders and small-for-gestational-age infants."Reproductive sciences (Thousand Oaks, Calif.)"More Details
    22519984 Monocyte-derived and CD34+/KDR+ endothelial progenitor cells in heart failure.Journal of thrombosis and haemostasis : JTHMore Details
    22855739 Osteocalcin positive CD133+/CD34-/KDR+ progenitor cells as an independent marker for unstable atherosclerosis.European heart journalMore Details
    23217199 Myocardial dysfunction in patients with type 2 diabetes mellitus: role of endothelial progenitor cells and oxidative stress.Cardiovascular diabetologyMore Details
    22474430 Procalcific phenotypic drift of circulating progenitor cells in type 2 diabetes with coronary artery disease.Experimental diabetes researchMore Details
    20080904 Role of circulating endothelial progenitor cells in patients with rheumatoid arthritis with coronary calcification.The Journal of rheumatologyMore Details
    20935001 Coronary endothelial dysfunction in humans is associated with coronary retention of osteogenic endothelial progenitor cells.European heart journalMore Details
    19729464 Synergistic effects of asymmetrical dimethyl-L-arginine accumulation and endothelial progenitor cell deficiency on renal function decline during a 2-year follow-up in stable angina."Nephrology, dialysis, transplantation : official publication of the European"More Details
    20364046 "Coincidence of moderately elevated N-terminal pro-B-type natriuretic peptide, endothelial progenitor cells deficiency and propensity to exercise-induced myocardial ischemia in stable angina."Disease markersMore Details
    21072182 Quantification of circulating endothelial progenitor cells using the modified ISHAGE protocol.PloS oneMore Details
    19717420 Identification of a coronary vascular progenitor cell in the human heart.Proceedings of the National Academy of Sciences of the United States of AmericaMore Details
    19244479 Chronic hypoxia attenuates VEGF signaling and angiogenic responses by downregulation of KDR in human endothelial cells.American journal of physiology. Cell physiologyMore Details
    18977801 Local vessel injury following percutaneous coronary intervention does not promote early mobilisation of endothelial progenitor cells in the absence of myocardial necrosis.Heart (British Cardiac Society)More Details
    17132814 Secoisolariciresinol diglucoside: relevance to angiogenesis and cardioprotection against ischemia-reperfusion injury.The Journal of pharmacology and experimental therapeuticsMore Details
    17707181 Polymorphisms of KDR gene are associated with coronary heart disease.Journal of the American College of CardiologyMore Details
    17255539 Vascular dysfunction and reduced circulating endothelial progenitor cells in young healthy UK South Asian men."Arteriosclerosis, thrombosis, and vascular biology"More Details
    16148285 Circulating endothelial progenitor cells and cardiovascular outcomes.The New England journal of medicineMore Details
    16039284 Endurance training increases the number of endothelial progenitor cells in patients with cardiovascular risk and coronary artery disease.AtherosclerosisMore Details
    15470196 Association of vascular endothelial growth factor (VEGF) and VEGF receptor gene polymorphisms with coronary artery lesions of Kawasaki disease.Pediatric researchMore Details
    15478946 Effects of ox-LDL on number and activity of circulating endothelial progenitor cells.Drug and chemical toxicologyMore Details

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



    PPI interactions

    There were totally 51 unique genes interacted with KDR. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ANXA5 Two-hybrid10329451|10329451|10329451 CHD related
    SHC2 Two-hybrid10749680|10749680,9790910 No
    PLXNA1 Affinity Capture-Western14977921 No
    CDH5 Affinity Capture-Western11950700 CHD related
    ACP1 Two-hybrid10608891 CHD related
    GRB2 Affinity Capture-Western10319320|10319320,16966330 CHD related
    RASA1 Affinity Capture-Western10319320|10319320 No
    PLCG1 Reconstituted Complex9398617 CHD related
    UBC Affinity Capture-Western15060076|19883397|21402774|17702744 No
    KDR in vitro;in vivo10749680,10579917,10368301 CHD related
    HSP90AA1 in vivo15247219 CHD related
    ITGB3 in vivo10022831 CHD related
    PTPN6 in vitro;in vivo9405464,16453023 No
    PTPN11 in vivo9405464 CHD related
    NCK1 in vitro;in vivo9405464,16966330 No
    GNA11 in vivo12670961 No
    GNAQ in vitro12670961 CHD related
    BMX in vivo14532277 No
    CSF2RB in vitro16007196 No
    FYN in vitro7929439 No
    YES1 in vitro7929439 No
    TIMP3 in vitro;in vivo12652295 CHD related
    CTNNB1 in vitro12920240 CHD related
    SYNGAP1 in vitro9405464 No
    SHB Affinity Capture-Western15026417|15026417 No
    FLT1 Biochemical Activity12796773 CHD related
    VEGFA Biochemical Activity12716911|8621427,17318185 CHD related
    SHC1 Affinity Capture-Western11950700|10749680 No
    FIGF Reconstituted Complex9435229|9435229 No
    GRB10 Two-hybrid11494124|11494124 No
    COL18A1 Reconstituted Complex12029087 No
    CBL Reconstituted Complex17372230|20011623|12649282 No
    AIMP2 Two-hybrid21900206 No
    FBXW11 Two-hybrid21900206 No
    BTRC Reconstituted Complex21402774|22711876 No
    CUL1 Affinity Capture-Western22711876 No
    CSNK1D Affinity Capture-Western22711876|22711876 No
    SRC Affinity Capture-Western19050761|18194650|10455194,16966330 CHD related
    IQGAP1 Affinity Capture-Western19050761 No
    PLCG2 in vivo9398617 No
    VEGFC in vivo11332691 No
    ATR in vitro;in vivo;yeast 2-hybrid10749680 No
    FLT4 in vitro15474514 No
    P2RY2 in vitro;in vivo15175347 No
    SH2D2A in vitro;yeast 2-hybrid10692392,15962004 No
    NRP1 in vitro;in vivo11333271,17222790,16763549 CHD related
    STAT1 in vitro;in vivo10961983 CHD related
    CAV1 in vitro12529448 CHD related
    DNM2 in vivo16049137 No
    FRS2 in vitro12154000 No
    CRK in vitro15051508 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00398SorafenibFor the treatment of patients with advanced renal cell carcinoma.L01XE05
    approvedDB01268SunitinibFor the treatment of advanced renal cell carcinoma as well as the treatment of gastrointestinal stromal tumor after disease progression on or intolerance to imatinib mesylate.L01XE04
    experimentalDB04727"N-(4-{4-AMINO-6-[4-(METHYLOXY)PHENYL]FURO[2,3-D]PYRIMIDIN-5-YL}PHENYL)-N'-[2-FLUORO-5-(TRIFLUOROMETHYL)PHENYL]UREA"
    experimentalDB069384-[[2-[[4-chloro-3-(trifluoromethyl)phenyl]amino]-3H-benzimidazol-5-yl]oxy]-N-methyl-pyridine-2-carboxamide
    experimentalDB07183N-(4-phenoxyphenyl)-2-[(pyridin-4-ylmethyl)amino]nicotinamide
    experimentalDB07274"N-cyclopropyl-6-[(6,7-dimethoxyquinolin-4-yl)oxy]naphthalene-1-carboxamide"
    experimentalDB07326"6-chloro-N-pyrimidin-5-yl-3-{[3-(trifluoromethyl)phenyl]amino}-1,2-benzisoxazole-7-carboxamide"
    experimentalDB07333"N-(CYCLOPROPYLMETHYL)-4-(METHYLOXY)-3-({5-[3-(3-PYRIDINYL)PHENYL]-1,3-OXAZOL-2-YL}AMINO)BENZENESULFONAMIDE"
    experimentalDB07334"N-[5-(ETHYLSULFONYL)-2-METHOXYPHENYL]-5-[3-(2-PYRIDINYL)PHENYL]-1,3-OXAZOL-2-AMINE"
    experimentalDB07514"3-(2-aminoquinazolin-6-yl)-1-(3,3-dimethylindolin-6-yl)-4-methylpyridin-2(1H)-one"
    experimentalDB075283-(2-aminoquinazolin-6-yl)-4-methyl-1-[3-(trifluoromethyl)phenyl]pyridin-2(1H)-one
    experimentalDB07537"N'-(6-aminopyridin-3-yl)-N-(2-cyclopentylethyl)-4-methyl-benzene-1,3-dicarboxamide"
    experimentalDB08042"N~4~-methyl-N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine"
    experimentalDB08519"N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine"