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: FBN1

    Description: fibrillin 1

    Entrez Gene ID: 2200

    SwissProt Acc Number: P35555

    RefSeq: NM_000138

    It was suspected to be CHD related:

    ..All patients had previously tested negative for mutations in the FBN1 and TGFBR2 genes..

    From PMID: 21248741, in Journal Eur J Hum Genet , 2011


    References

    There were 3 potential papers with FBN1 and CHD.

    PMIDTitleJournalsDetails
    23951402 An integrative computational analysis provides evidence for FBN1-associated network deregulation in trisomy 21.Biology openMore Details
    21248741 Three novel mutations in the ACTA2 gene in German patients with thoracic aortic aneurysms and dissections.European journal of human genetics : EJHGMore Details
    18505769 Serial analysis of the vascular endothelial transcriptome under static and shear stress conditions.Physiological genomicsMore Details

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



    PPI interactions

    There were totally 13 unique genes interacted with FBN1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    MFAP2 Reconstituted Complex11481325 No
    CALR in vivo10547375 No
    HSPG2 in vitro15657057 No
    FBN2 in vivo10359653,10504303 No
    DCN in vivo10793130 CHD related
    FBLN2 Reconstituted Complex8702639|8702639,9886271 No
    MYOC Reconstituted Complex11923248|11923248 No
    VCAN Reconstituted Complex11726670 CHD related
    ELN Reconstituted Complex10825173 CHD related
    ATXN7 Two-hybrid21078624 No
    SPRY2 Two-hybrid21900206 No
    LTBP1 in vitro;in vivo12429738 CHD related
    MFAP5 in vivo12122015 No


    Involved FDA drugs

    There was no drug associated with FBN1