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: SCNN1B

    Description: "sodium channel, nonvoltage-gated 1, beta"

    Entrez Gene ID: 6338

    SwissProt Acc Number: P51168

    RefSeq: NM_000336

    It was suspected to be CHD related:

    .."We present such a method that extracts G x E information in longitudinal data of endophenotypes, and apply the method to repeated measures of multiple phenotypes related to coronary heart disease in Genetic Analysis Workshop 16 Problem 2. The new method identified many genes, including SCNN1B (sodium channel nonvoltage-gated 1 beta) and PKP2 (plakophilin 2), with potential time-dependent G x E interactions;"..

    From PMID: 20018082, in Journal BMC Proc. , 2009


    References

    There were 0 potential papers with SCNN1B and CHD.

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



    PPI interactions

    There were totally 21 unique genes interacted with SCNN1B. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    NEDD4 Reconstituted Complex10642508|11244092|20237237 No
    NEDD4L Far Western11244092|16416336 No
    HECW1 Far Western11244092 No
    ITCH Far Western11244092 No
    UBC Affinity Capture-Western18322022|17502380|17381423|16574660|20237237|19380724|18701608 No
    EPN1 Affinity Capture-Western16574660 No
    SGK1 Affinity Capture-Western20237237 No
    USP2 Affinity Capture-Western18701608 No
    SCNN1G PCA22526458 No
    SCNN1A PCA22526458|22526458|8986818 CHD related
    SERP1 PCA22526458|22526458 No
    ANK3 in vivo11997395 No
    NFASC in vivo11470829 No
    STX1A Affinity Capture-Western14996668 No
    WWP2 Reconstituted Complex12167593|12167593 No
    AP1M2 Affinity Capture-Western16574660 No
    COMMD1 Affinity Capture-Western20237237|14645214 No
    RAF1 Affinity Capture-Western19380724 CHD related
    TSC22D3 Affinity Capture-Western19380724 No
    SCNN1D in vivo7499195 No
    CNTN1 in vivo14761957,11567041 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00384Triamterene"For the treatment of edema associated with congestive heart failure, cirrhosis of the liver, and the nephrotic syndrome; also in steroid-induced edema, idiopathic edema, and edema due to secondary hyperaldosteronism."C03DB02
    approvedDB00594AmilorideFor use as adjunctive treatment with thiazide diuretics or other kaliuretic-diuretic agents in congestive heart failure or hypertension.C03DB01