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: CBS

    Description: cystathionine-beta-synthase

    Entrez Gene ID: 875

    SwissProt Acc Number: P35520

    RefSeq: NM_000071

    It was suspected to be CHD related:

    .."Our results not only highlight the involvement of the MSR and CBS genes in the etiology of cardiovascular disease, but also emphasize the strength of haplotype analyses in association studies."..

    From PMID: 17553479, in Journal Clin Biochem. , 2007


    References

    There were 18 potential papers with CBS and CHD.

    PMIDTitleJournalsDetails
    23824729 Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.The American journal of clinical nutritionMore Details
    22738689 Peripheral blood gene expression profile of atherosclerotic coronary artery disease in patients of different ethnicity in Malaysia.Journal of cardiologyMore Details
    21669881 Exploration of the difference in incidence of renal replacement therapy between Flanders and the Netherlands--investigation of explanatory variables."Nephrology, dialysis, transplantation : official publication of the European"More Details
    23166827 Hydrogen sulfide in paraventricular nucleus enhances sympathetic activity and cardiac sympathetic afferent reflex in chronic heart failure rats.PloS oneMore Details
    21567207 Tetra primer ARMS-PCR relates folate/homocysteine pathway genes and ACE gene polymorphism with coronary artery disease.Molecular and cellular biochemistryMore Details
    21372285 Peptide-mediated disruption of calmodulin-cyclin E interactions inhibits proliferation of vascular smooth muscle cells and neointima formation.Circulation researchMore Details
    20175737 Cystathionine beta-synthase 844Ins68 polymorphism is not associated with the levels of homocysteine and cysteine in an Indian population."Biomarkers : biochemical indicators of exposure, response, and susceptibility to "More Details
    19577940 Polygenic association with total homocysteine in the post-folic acid fortification era: the CARDIA study.Molecular genetics and metabolismMore Details
    19406869 "Myocardial bridging, a frequent component of the hypertrophic cardiomyopathy phenotype, lacks systematic association with sudden cardiac death."European heart journalMore Details
    19028542 Resveratrol supplementation worsen the dysregulation of genes involved in hepatic lipid homeostasis observed in hyperhomocysteinemic mice.Food and chemical toxicology : an international journal published for the BritishMore Details
    18620331 "[Effect of polymorphisms on key enzymes in homocysteine metabolism, on plasma homocysteine level and on coronary artery-disease risk in a Tunisian population]."Annales de cardiologie et d'angeiologieMore Details
    17553479 A CBS haplotype and a polymorphism at the MSR gene are associated with cardiovascular disease in a Spanish case-control study.Clinical biochemistryMore Details
    18020970 Hyperhomocysteinemia and high-density lipoprotein metabolism in cardiovascular disease.Clinical chemistry and laboratory medicine : CCLM / FESCCMore Details
    16194201 Modeling premature occurrence of acute coronary syndrome with atherogenic and thrombogenic risk factors and gene markers in extended families.Journal of thrombosis and haemostasis : JTHMore Details
    16259797 The influence of genetic and environmental factors on plasma homocysteine concentrations in a population at high risk for coronary artery disease.Annals of clinical biochemistryMore Details
    12051965 "S-adenosylhomocysteine, but not homocysteine, is toxic to yeast lacking cystathionine beta-synthase."Molecular genetics and metabolismMore Details
    11292330 Genetic variation of the methylenetetrahydrofolate reductase and cystathionine beta-synthase genes in Korean patients with coronary artery disease and a new polymorphism in intron 7.Molecular and cellular probesMore Details
    10833331 Polymorphisms in the CBS gene associated with decreased risk of coronary artery disease and increased responsiveness to total homocysteine lowering by folic acid.Molecular genetics and metabolismMore Details

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



    PPI interactions

    There were totally 10 unique genes interacted with CBS. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    VTA1 Two-hybrid16189514|16189514 No
    FXR2 Two-hybrid16189514|16189514 No
    C17orf28 Two-hybrid16189514|16189514 No
    CBS Two-hybrid16189514|16189514|11483494|11173483|21900206|11173483,11483494,12173932,16189514 CHD related
    HSP26 Synthetic Rescue20066033 No
    HTT in vivo;yeast 2-hybrid9466992,10434301 No
    HGS Reconstituted Complex19019082 No
    UBC Affinity Capture-MS16196087|22118674|18781797|21139048|21890473 No
    PRKAR1A Two-hybrid21900206 CHD related
    CDK2 Affinity Capture-MS21319273 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    nutraceuticalDB00114Pyridoxal PhosphateFor nutritional supplementation and for treating dietary shortage or imbalance.A11HA02;A11HA06
    approved;nutraceuticalDB00118S-Adenosylmethionine"S-Adenosylmethionine (SAMe) is used as a drug in Europe for the treatment of depression, liver disorders, fibromyalgia, and osteoarthritis. It has also been introduced into the United States market as a dietary supplement for the support of bone and joint health, as well as mood and emotional well being."
    approved;nutraceuticalDB00133L-SerineUsed as a natural moisturizing agent in some cosmetics and skin care products.
    approved;nutraceuticalDB00151L-CysteineFor the prevention of liver damage and kidney damage associated with overdoses of acetaminophenR05CB01;S01XA08;V03AB23
    approved;nutraceuticalDB00165PyridoxineFor the treatment of vitamin B6 deficiency and for the prophylaxis of isoniazid-induced peripheral neuropathy.A11HA02
    experimentalDB03014Heme