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: NOS1

    Description: nitric oxide synthase 1 (neuronal)

    Entrez Gene ID: 4842

    SwissProt Acc Number: P29475

    RefSeq: NM_000620

    It was suspected to be CHD related:

    ..NOS1 and NOS3 were abnormally regulated in the heart of TK(-/-) mice after MI...

    From PMID: 18343196, in Journal Eur J Heart Fail , 2008


    References

    There were 2 potential papers with NOS1 and CHD.

    PMIDTitleJournalsDetails
    18343196 Tissue kallikrein deficiency aggravates cardiac remodelling and decreases survival after myocardial infarction in mice.European journal of heart failureMore Details
    14510775 From molecules to mammals: what's NOS got to do with it?Acta physiologica ScandinavicaMore Details

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



    PPI interactions

    There were totally 36 unique genes interacted with NOS1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    Ctbp1 Affinity Capture-MS11590170 No
    NOS1AP Two-hybrid9459447|9459447|9459447 CHD related
    DLG4 Affinity Capture-Western9459447|8625413|8625413 No
    DLG2 Two-hybrid8625413 No
    UBC Affinity Capture-Western15466472|10751385|20729196 No
    HSPA4 Affinity Capture-Western15466472 No
    SUMO1 Affinity Capture-Western21545853|21545853 No
    ATP2B4 in vitro;in vivo11591728 CHD related
    VAC14 in vitro;in vivo17161399 No
    ADRA1A in vivo12184796 CHD related
    ADRA1D in vivo12184796 CHD related
    ADRA1B in vivo12184796 CHD related
    ADRB1 in vivo12184796 CHD related
    ADRB2 in vivo12184796 CHD related
    HMOX1 in vivo11849436 CHD related
    ZDHHC23 Affinity Capture-Western15105416|15105416|15105416 No
    RASD1 Reconstituted Complex11086993|11086993 No
    BDKRB2 Affinity Capture-Western10681501 CHD related
    PTPN6 Affinity Capture-Western11511520|11511520 No
    SYN1 Reconstituted Complex11867766 No
    SNTA1 Reconstituted Complex9412493|11747091,10221915 No
    CAV1 Reconstituted Complex9353265 CHD related
    STUB1 Biochemical Activity15466472|20729196 No
    HDAC1 Negative Genetic22318606 CHD related
    HSP90AA1 in vitro;in vivo11284722,9880522 CHD related
    PFKM in vitro10187848 No
    PRKCA in vitro10400690,10874031,12630910,1375933 CHD related
    ARG1 in vivo11849441 CHD related
    CAV3 in vitro9353265 CHD related
    PRKACA in vitro10400690,10874031,12630910,1375933 CHD related
    PTPRN in vitro;in vivo11043403 No
    CTBP1 in vitro;in vivo11590170 No
    CAMK1 in vitro;in vivo10400690,10874031,12630910,1375933,15251453 No
    CAMK2A in vitro10400690,10874031,12630910,1375933 CHD related
    CAMK4 in vitro10400690,10874031,12630910,1375933 No
    DLGAP2 in vitro10824095 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00155L-Citrulline"Used for nutritional supplementation, also for treating dietary shortage or imbalance."
    experimentalDB01821"L-N(Omega)-Nitroarginine-2,4-L-Diaminobutyric Amide"
    experimentalDB01942Formic Acid
    experimentalDB019973-Bromo-7-Nitroindazole
    experimentalDB02027N-{(4s)-4-Amino-5-[(2-Aminoethyl)Amino]Pentyl}-N'-Nitroguanidine
    experimentalDB02044N-(3-(Aminomethyl)Benzyl)Acetamidine
    experimentalDB02077L-N(Omega)-Nitroarginine-(4r)-Amino-L-Proline Amide
    experimentalDB02143N-Isopropyl-N'-Hydroxyguanidine
    experimentalDB02644N-Omega-Propyl-L-Arginine
    experimentalDB02692"(6r,1'r,2's)-5,6,7,8 Tetrahydrobiopterin"
    experimentalDB02727N-Butyl-N'-Hydroxyguanidine
    experimentalDB02944Alpha-D-Mannose
    experimentalDB02991S-Ethyl-N-[4-(Trifluoromethyl)Phenyl]Isothiourea
    experimentalDB03014Heme
    experimentalDB03144N-Omega-Hydroxy-L-Arginine
    experimentalDB03147Flavin-Adenine Dinucleotide
    experimentalDB03247Riboflavin Monophosphate
    experimentalDB03449N-(4-(2-((3-Chlorophenylmethyl)Amino)Ethyl)Phenyl)-2-Thiophecarboxamidine
    experimentalDB034612'-Monophosphoadenosine 5'-Diphosphoribose
    experimentalDB03707S-Ethyl-N-Phenyl-Isothiourea
    experimentalDB03710N5-(1-Imino-3-Butenyl)-L-Ornithine
    experimentalDB038925-N-Allyl-Arginine
    experimentalDB04223Nitroarginine
    experimentalDB08018"N-{(3S,4S)-4-[(6-AMINO-4-METHYLPYRIDIN-2-YL)METHYL]PYRROLIDIN-3-YL}-N'-(4-CHLOROBENZYL)ETHANE-1,2-DIAMINE"
    experimentalDB08019"N-{(3R,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-(3-chlorobenzyl)ethane-1,2-diamine"