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: NOS2

    Description: "nitric oxide synthase 2, inducible"

    Entrez Gene ID: 4843

    SwissProt Acc Number: P35228

    RefSeq: NM_000625

    It was suspected to be CHD related:

    ..A significant increase of vascular occlusion in NOS2-knockout mice demonstrated an antiarteriosclerotic effect of NOS2..

    From PMID: 11151787, in Journal Z Kardiol. , 2000


    References

    There were 3 potential papers with NOS2 and CHD.

    PMIDTitleJournalsDetails
    23397596 Endothelial NOS (NOS3) impairs myocardial function in developing sepsis.Basic research in cardiologyMore Details
    18818404 Inducible nitric oxide synthase expression and cardiomyocyte dysfunction during sustained moderate ischemia in pigs.Circulation researchMore 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 17 unique genes interacted with NOS2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SLC9A3R1 Reconstituted Complex12080081 No
    RAC1 Reconstituted Complex11457725 CHD related
    SPSB1 Affinity Capture-Western21199876|21199876|21549100 No
    SPSB4 Affinity Capture-Western21199876 No
    UBC Affinity Capture-Western21199876|21549100|19376148|20634424|21094287|18955503 No
    SPSB2 Affinity Capture-Western21199876|21549100 No
    TCEB1 Affinity Capture-Western21199876 No
    CUL5 Affinity Capture-Western21199876 No
    UCHL5 Affinity Capture-Western20634424 No
    STUB1 Affinity Capture-Western18955503 No
    ACTB in vitro12080081 No
    NOS2 in vitro;in vivo10409685,14614131 CHD related
    CAV1 Co-fractionation11114180|11114180|11114180 CHD related
    RAC2 Affinity Capture-Western11457725 No
    RNF7 Biochemical Activity20603330 No
    SRC in vitro16116474 CHD related
    ACTN4 in vitro12960352 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00125L-Arginine"Used for nutritional supplementation, also for treating dietary shortage or imbalance."B05XB01
    approved;nutraceuticalDB00155L-Citrulline"Used for nutritional supplementation, also for treating dietary shortage or imbalance."
    approvedDB01110Miconazole"For topical application in the treatment of tinea pedis (athlete’s foot), tinea cruris, and tinea corporis caused by <i>Trichophyton rubrum</i>, <i>Trichophyton mentagrophytes</i>, and <i>Epidermophyton floccosum</i>, in the treatment of cutaneous candidiasis (moniliasis), and in the treatment of tinea versicolor."A01AB09;A07AC01;D01AC02;G01AF04;J02AB01;S02AA13
    approvedDB01234DexamethasoneA01AC02;C05AA09;D07AB19;D07XB05;D10AA03;H02AB02;R01AD03;S01BA01;S01CB01;S02BA06;S03BA01;
    experimentalDB01686"N,N-dimethylarginine"
    experimentalDB018354r-Fluoro-N6-Ethanimidoyl-L-Lysine
    experimentalDB019973-Bromo-7-Nitroindazole
    experimentalDB02044N-(3-(Aminomethyl)Benzyl)Acetamidine
    experimentalDB022077-Nitroindazole
    experimentalDB02234Ethylisothiourea
    experimentalDB02462Thiocoumarin
    experimentalDB02533Aminoguanidine
    experimentalDB02539S-Ethylisothiourea
    experimentalDB02644N-Omega-Propyl-L-Arginine
    experimentalDB02692"(6r,1'r,2's)-5,6,7,8 Tetrahydrobiopterin"
    experimentalDB03014Heme
    experimentalDB031006-Nitroindazole
    experimentalDB03144N-Omega-Hydroxy-L-Arginine
    experimentalDB03271"7,8-Dihydro-L-Biopterin"
    experimentalDB03449N-(4-(2-((3-Chlorophenylmethyl)Amino)Ethyl)Phenyl)-2-Thiophecarboxamidine
    experimentalDB03953L-Thiocitrulline
    experimentalDB04400"7,8-Dihydrobiopterin"
    experimentalDB045345-Nitroindazole
    experimentalDB06879"5-(4'-AMINO-1'-ETHYL-5',8'-DIFLUORO-1'H-SPIRO[PIPERIDINE-4,2'-QUINAZOLINE]-1-YLCARBONYL)PICOLINONITRILE"
    experimentalDB06916"N-[2-(1,3-BENZODIOXOL-5-YL)ETHYL]-1-[2-(1H-IMIDAZOL-1-YL)-6-METHYLPYRIMIDIN-4-YL]-D-PROLINAMIDE"
    experimentalDB070024-({4-[(4-methoxypyridin-2-yl)amino]piperidin-1-yl}carbonyl)benzonitrile
    experimentalDB07003"(2S)-2-methyl-2,3-dihydrothieno[2,3-f][1,4]oxazepin-5-amine"
    experimentalDB07007"(3R)-3-[(1,2,3,4-tetrahydroisoquinolin-7-yloxy)methyl]-2,3-dihydrothieno[2,3-f][1,4]oxazepin-5-amine"
    experimentalDB07008"4-(1,3-BENZODIOXOL-5-YLOXY)-2-[4-(1H-IMIDAZOL-1-YL)PHENOXY]PYRIMIDINE"
    experimentalDB07011"(3S)-1-(1,3-BENZODIOXOL-5-YLMETHYL)-3-[4-(1H-IMIDAZOL-1-YL)PHENOXY]PIPERIDINE"
    experimentalDB07029"4-(1,3-BENZODIOXOL-5-YLOXY)-2-[4-(1H-IMIDAZOL-1-YL)PHENOXY]-6-METHYLPYRIMIDINE"
    experimentalDB07306ETHYL 4-[(4-CHLOROPYRIDIN-2-YL)AMINO]PIPERIDINE-1-CARBOXYLATE
    experimentalDB07318"N-[2-(4-AMINO-5,8-DIFLUORO-1,2-DIHYDROQUINAZOLIN-2-YL)ETHYL]-3-FURAMIDE"
    experimentalDB07388ETHYL 4-[(4-METHYLPYRIDIN-2-YL)AMINO]PIPERIDINE-1-CARBOXYLATE
    experimentalDB07389N-[2-(6-AMINO-4-METHYLPYRIDIN-2-YL)ETHYL]-4-CYANOBENZAMIDE
    experimentalDB07405"1-(6-CYANO-3-PYRIDYLCARBONYL)-5',8'-DIFLUOROSPIRO[PIPERIDINE-4,2'(1'H)-QUINAZOLINE]-4'-AMINE"
    experimentalDB082144-(1H-IMIDAZOL-1-YL)PHENOL
    experimentalDB08750"1-[4-(AMINOMETHYL)BENZOYL]-5'-FLUORO-1'H-SPIRO[PIPERIDINE-4,2'-QUINAZOLIN]-4'-AMINE"
    approvedDB08814TriflusalB01AC18