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: EGF

    Description: epidermal growth factor (beta-urogastrone)

    Entrez Gene ID: 1950

    SwissProt Acc Number: P01133

    RefSeq: NM_001963

    It was suspected to be CHD related:

    ..The epidermal growth factor (EGF) receptors HER2 and HER4 and the ligands HB-EGF and NRG1 are crucial for heart development...

    From PMID: 22792252, in Journal PLoS One , 2012


    References

    There were 15 potential papers with EGF and CHD.

    PMIDTitleJournalsDetails
    23984427 Growth factors serum levels in coronary artery disease patients scheduled for bypass surgery: perioperative dynamics and comparisons with healthy volunteers.BioMed research internationalMore Details
    22371488 Urine proteome analysis reflects atherosclerotic disease in an ApoE-/- mouse model and allows the discovery of new candidate biomarkers in mouse and human atherosclerosis.Molecular & cellular proteomics : MCPMore Details
    22792252 Hypoxia changes the expression of the epidermal growth factor (EGF) system in human hearts and cultured cardiomyocytes.PloS oneMore Details
    21067705 Mechanisms of myogenic tone of coronary arteriole: Role of down stream signaling of the EGFR tyrosine kinase.Microvascular researchMore Details
    19342596 Amplification of coronary arteriogenic capacity of multipotent stromal cells by epidermal growth factor."Arteriosclerosis, thrombosis, and vascular biology"More Details
    19001363 Structural and biochemical characterization of the wild type PCSK9-EGF(AB) complex and natural familial hypercholesterolemia mutants.The Journal of biological chemistryMore Details
    18280808 Cytokine elevations in acute coronary syndrome and ovarian cancer: a mechanism for the up-regulation of the acute phase proteins in these different disease etiologies.Clinical biochemistryMore Details
    18499674 Influences of the N700S thrombospondin-1 polymorphism on protein structure and stability.The Journal of biological chemistryMore Details
    18375753 Human CMV infection of endothelial cells induces an angiogenic response through viral binding to EGF receptor and beta1 and beta3 integrins.Proceedings of the National Academy of Sciences of the United States of AmericaMore Details
    17293495 Endogenous interleukin-1 alpha promotes a proliferative and proinflammatory phenotype in human vascular smooth muscle cells.American journal of physiology. Heart and circulatory physiologyMore Details
    17924848 Cytokines and growth factors in mostly atherosclerotic patients on hemodialysis determined by biochip array technology.Clinical chemistry and laboratory medicine : CCLM / FESCCMore Details
    16877529 Heparin binding EGF is necessary for vasospastic response to endothelin.FASEB journal : official publication of the Federation of American Societies for More Details
    12138120 Role of adiponectin in preventing vascular stenosis. The missing link of adipo-vascular axis.The Journal of biological chemistryMore Details
    11922634 Increased plasma HB-EGF associated with obesity and coronary artery disease.Biochemical and biophysical research communicationsMore Details
    10916078 Angiotensin II-induced growth of vascular smooth muscle cells requires an Src-dependent activation of the epidermal growth factor receptor.Kidney internationalMore Details

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



    PPI interactions

    There were totally 22 unique genes interacted with EGF. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    EGF Co-crystal Structure11438527|9188692,11438527 CHD related
    EGFR Reconstituted Complex12093292 CHD related
    ERBB2 Reconstituted Complex12093292 CHD related
    ERBB3 Reconstituted Complex12093292 No
    PIK3R2 Reconstituted Complex1334406|1334406 No
    LMNA Two-hybrid16248985 CHD related
    PCGF2 Affinity Capture-Western19727227 No
    GRB2 in vivo10973965 CHD related
    FNBP1 Co-localization15252009 No
    RPS6KA5 Phenotypic Enhancement9687510 No
    MAPKAPK2 Phenotypic Enhancement9687510 No
    VTN Reconstituted Complex11796824|11796824 CHD related
    ZFYVE28 Co-localization19460345 No
    LMNB1 Affinity Capture-Western19727227 No
    SREBF1 Affinity Capture-Western19727227 No
    EMD Affinity Capture-Western19727227 No
    UBE2I Affinity Capture-Western19727227 No
    CPM in vivo7615511,8796265 No
    ADAM12 in vivo11786904 CHD related
    ADRBK1 in vivo15620700 CHD related
    NRG1 in vitro7730382 CHD related
    DUSP3 in vitro1281549 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00364Sucralfate"For the short-term treatment (up to 8 weeks) of active duodenal ulcer, as well as maintenance therapy for duodenal ulcer patients at reduced dosage (1 gram twice a day) after healing of acute ulcers. Also used for the short-term treatment of gastric ulcer."A02BX02
    experimentalDB04454Alpha-Aminobutyric Acid