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: SCARB1

    Description: "scavenger receptor class B, member 1"

    Entrez Gene ID: 949

    SwissProt Acc Number: Q8WTV0

    RefSeq: NM_001082959

    It was suspected to be CHD related:

    .."Lipoprotein-associated phospholipase A2 (Lp-PLA2) generates proinflammatory and proatherogenic compounds in the arterial vascular wall and is a potential therapeutic target in coronary heart disease (CHD). Variants at six loci were associated with Lp-PLA2 activity (PLA2G7, APOC1, CELSR2, LDL, ZNF259, SCARB1)"..

    From PMID: 22003152, in Journal Eur?Heart?J.? , 2012


    References

    There were 10 potential papers with SCARB1 and CHD.

    PMIDTitleJournalsDetails
    23919842 "Association between APOE, SCARB1, PPARalpha polymorphisms and serum lipids in a population of Lithuanian adults."Lipids in health and diseaseMore Details
    23510561 SCARB1 single nucleotide polymorphism (rs5888) is associated with serum lipid profile and myocardial infarction in an age- and gender-dependent manner.Lipids in health and diseaseMore Details
    24151447 Scavenger receptor class B type 1 gene rs5888 single nucleotide polymorphism and the risk of coronary artery disease and ischemic stroke: a case-control study.International journal of medical sciencesMore Details
    22003152 Eight genetic loci associated with variation in lipoprotein-associated phospholipase A2 mass and activity and coronary heart disease: meta-analysis of genome-wide association studies from five community-based studies.European heart journalMore Details
    23041084 "Association of three polymorphisms of scavenger receptor class BI gene (exon8, exon1, intron5) with coronary stenosis in a coronary Tunisian population."GeneMore Details
    22229114 Common Variants in 6 Lipid-Related Genes Discovered by High-Resolution DNA Melting Analysis and Their Association with Plasma Lipids.Journal of clinical & experimental cardiologyMore Details
    20160195 Association of scavenger receptor class B type I polymorphisms with subclinical atherosclerosis: the Multi-Ethnic Study of Atherosclerosis.Circulation. Cardiovascular geneticsMore Details
    20686565 "Biological, clinical and population relevance of 95 loci for blood lipids."NatureMore Details
    17312010 Robust immunohistochemical staining of several classes of proteins in tissues subjected to autolysis.The journal of histochemistry and cytochemistry : official journal of theMore Details
    17618962 Scavenger receptor class B type I polymorphisms and peripheral arterial disease.Metabolism: clinical and experimentalMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with SCARB1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    APOA1 Reconstituted Complex10764676|1076467 CHD related
    APOA2 Reconstituted Complex10764676 CHD related
    APOE in vitro;in vivo12138091 CHD related
    PDZK1 Affinity Capture-Western12119305|10829064,14551195,12119305 CHD related
    UBC Affinity Capture-MS18781797|21987572|21139048|21890473|21906983 No
    CUL1 Affinity Capture-MS21145461 No
    CAND1 Affinity Capture-MS21145461 No
    FBXO6 Affinity Capture-MS22268729 No
    PEX5 in vivo14652019 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00144Phosphatidylserine"Phosphatidylserine has demonstrated some usefulness in treating cognitive impairment, including Alzheimer's disease, age-associated memory impairment and some non-Alzheimer's dementias. More research is needed before phosphatidylserine can be indicated for immune enhancement or for reduction of exercise stress."