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: JAK2

    Description: Janus kinase 2

    Entrez Gene ID: 3717

    SwissProt Acc Number: O60674

    RefSeq: NM_004972

    It was suspected to be CHD related:

    ..G-CSF attenuated myocardial apoptosis induced by CME via JAK2/STAT3 pathway...

    From PMID: 19099985, in Journal Zhonghua Xin Xue Guan Bing Za Zhi , 2008


    References

    There were 11 potential papers with JAK2 and CHD.

    PMIDTitleJournalsDetails
    22686448 Acute ST-segment elevation myocardial infarction: a rare initial presentation of previously undiagnosed essential thrombocythemia.PlateletsMore Details
    20306156 "The development of gastric cancer in a patient with polycythemia Vera, 3P deletion, and JAK2 V617F mutation."Journal of gastrointestinal cancerMore Details
    19478480 JAK2 V617F-positive latent essential thrombocythemia and splanchnic vein thrombosis: the role of bone marrow biopsy for the diagnosis of myeloproliferative disease.Acta haematologicaMore Details
    18298949 Amlodipine inhibits cell proliferation via PKD1-related pathway.Biochemical and biophysical research communicationsMore Details
    18355530 Granulocyte colony-stimulating factor prevents reperfusion injury after heart preservation.The Annals of thoracic surgeryMore Details
    17158356 Sphingosine-1-phosphate stimulates the functional capacity of progenitor cells by activation of the CXCR4-dependent signaling pathway via the S1P3 receptor."Arteriosclerosis, thrombosis, and vascular biology"More Details
    17210076 Essential thrombocythemia.Orphanet journal of rare diseasesMore Details
    15886225 Leptin-mediated activation of human platelets: involvement of a leptin receptor and phosphodiesterase 3A-containing cellular signaling complex.American journal of physiology. Endocrinology and metabolismMore Details
    15927298 Leptin potentiates ADP-induced [Ca(2+)](i) increase via JAK2 and tyrosine kinases in a megakaryoblast cell line.Diabetes research and clinical practiceMore Details
    15454281 Vitamin C inhibits hypoxia-induced damage and apoptotic signaling pathways in cardiomyocytes and ischemic hearts.Free radical biology & medicineMore Details
    11162135 Myocardial ischemia activates the JAK-STAT pathway through angiotensin II signaling in in vivo myocardium of rats.Journal of molecular and cellular cardiologyMore Details

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



    PPI interactions

    There were totally 103 unique genes interacted with JAK2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PRMT5 Two-hybrid10531356|21316606|21316606 No
    SOCS1 Two-hybrid10064597|9202126|11971965|9344848|14522994|11314018|19287004 CHD related
    EPOR Affinity Capture-Western11779507|8343951|11779507,8343951,12441334 No
    SH2B2 Biochemical Activity10374881 No
    HSPA8 Affinity Capture-Western11679576 CHD related
    TEC Affinity Capture-Western9178903 No
    PTPN12 Affinity Capture-Western11731619 No
    CSF2RB Reconstituted Complex7775438|10772872 No
    VAV1 Affinity Capture-Western9162069|9162069|7530656 No
    SIRPA Affinity Capture-Western10842184|10842184 No
    IRS1 Biochemical Activity9492017|11208867|12960006 CHD related
    GRB2 Affinity Capture-Western7500025|7500025 CHD related
    EGFR Affinity Capture-Western10358079|9363897,10635327 CHD related
    PTK2B Affinity Capture-Western11818507 No
    PPP2R4 Affinity Capture-Western8702385 No
    PIK3R1 Affinity Capture-Western8702385 CHD related
    SOCS3 Affinity Capture-Western10882725|10421843|10421843|9344848|15514089 CHD related
    PTPN6 Affinity Capture-Western8943354|10772872 No
    HTR2A Affinity Capture-Western9169451 No
    SH2B1 Two-hybrid9343427|12551917,10757801,9343427 CHD related
    PPP2R1B Affinity Capture-Western11440634 No
    TUB Biochemical Activity10455176 No
    TSHR Affinity Capture-Western10809230 No
    STAT3 Affinity Capture-Western9211920|10925297,11940572,11294897,10918587,12244095,11350938,12626508,8626374,12576423,14551213 CHD related
    STAM Biochemical Activity9133424 No
    UBC Affinity Capture-Western11278610|21119685|14522994|21685897|19543316 No
    STAT1 Affinity Capture-Western20353823|7657660,11294897,10918587,15322115,7543024,11839738,12817007,7690989,12637327,11152457 CHD related
    HSP90AA1 Affinity Capture-Western20353823 CHD related
    HSP90AB1 Affinity Capture-Western20353823 CHD related
    SKP2 Affinity Capture-Western21119685 No
    GTF2I Biochemical Activity11313464|9837922,9012831,11373296,11313464,11934902 No
    HIST3H3 Biochemical Activity19783980 No
    CDKN1B Biochemical Activity21423214|21423214 CHD related
    MAP3K5 Affinity Capture-Western19287004|19287004 CHD related
    FES in vivo8631962 No
    PLCG2 in vivo14978237 No
    IRS2 in vivo12960006 CHD related
    MPL in vitro;in vivo10979953,7534285,10224114,10918061 No
    NFKBIA in vitro11493922 CHD related
    PDGFRB in vitro;in vivo8657151,9484840 No
    IL3RA in vivo15988755 No
    MST1R in vivo14982882 No
    PPP2CA in vitro;in vivo11440634 CHD related
    HES5 in vitro;in vivo15156153 No
    CSF3R in vitro;in vivo7775438 No
    JAK2 in vitro;in vivo9516124,9111318,11593427,15143187,11818507,7889566,15143188,15121872,17027227 CHD related
    CCR2 in vitro;in vivo9670957 CHD related
    STAP2 in vivo12540842 No
    AGTR1 in vivo7746328 CHD related
    PPIA Affinity Capture-Western12668872 CHD related
    IL12RB2 Reconstituted Complex10198225|10198225 No
    FYN Affinity Capture-Western10551884|10551884 No
    STAT5A Affinity Capture-Western9575217 No
    STAT5B Affinity Capture-Western9575217 No
    CXCR4 Affinity Capture-Western10506573|10506573 CHD related
    DNAJA3 Affinity Capture-Western11679576|11679576 No
    PTK2 Affinity Capture-Western9553131|10925297|9553131,10925297 No
    GHR Affinity Capture-Western7540178|8063815|10502458|21347402|7540178,10502458,8063815 CHD related
    BRCA1 Affinity Capture-Western11163768 CHD related
    PTPN11 Reconstituted Complex8995399|7559603,8912646,8995399 CHD related
    YES1 Affinity Capture-Western8702385|8702385 No
    TNFRSF1A Reconstituted Complex9510175|9510175|9510175 CHD related
    LYN Reconstituted Complex9573010|9573010 No
    ERBB2 Affinity Capture-Western11940572|11940572 CHD related
    ELP2 Affinity Capture-Western10954736|10954736 No
    KIT Affinity Capture-Western7527392|9355737,8611693,7527392 No
    RAF1 Reconstituted Complex8876196 CHD related
    IL5RA Affinity Capture-Western9516124|9516124|9516124 No
    IFNGR1 Affinity Capture-Western7673114|21689637|21689637 No
    IFNGR2 Reconstituted Complex7673114 No
    CCR5 Affinity Capture-Western11278738|11591716 CHD related
    PRLR Affinity Capture-Western9202403|10772872 No
    IL6ST Affinity Capture-Western9388212 CHD related
    SHC1 Reconstituted Complex7535773|9126968|7535773,9126968 No
    GRB10 Affinity Capture-Western9632636|9632636 No
    INSR Affinity Capture-Western8912646|12456798 No
    PTPN1 Affinity Capture-Western11694501|11694501 CHD related
    STAM2 Affinity Capture-Western10899310|10899310 No
    IL2RB Affinity Capture-Western9553136 No
    CTLA4 Affinity Capture-Western10842319 CHD related
    ALK Affinity Capture-MS14968112 No
    IKBKG Reconstituted Complex20098747 No
    FGFR1 Affinity Capture-Western20388777 No
    ASB2 Affinity Capture-Western21119685 No
    HIST2H3C Affinity Capture-Western21689637 No
    VHL Affinity Capture-Western21685897 No
    PKD1 in vitro12007403 CHD related
    STAT2 in vivo7746328 No
    CRLF2 in vitro10872831 No
    HES1 in vitro;in vivo15156153 No
    IGF1R in vitro10747872,9492017 CHD related
    IL4R in vivo8609418 CHD related
    BCR in vitro;in vivo12370803,12023981 CHD related
    PTPRC in vitro11201744 CHD related
    MDK in vitro9452495 CHD related
    ABL1 in vitro;in vivo9111318,11593427,15143187 No
    JAK3 in vivo11585385 No
    LEPR in vitro8608603 CHD related
    VCP in vitro;in vivo11087817 No
    PPP2R5A in vitro8702385 No
    OSMR in vivo10586060 No
    IL23R in vitro;in vivo12023369 No
    UBASH3B in vitro;in vivo12370296 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB04716"2-(1,1-DIMETHYLETHYL)9-FLUORO-3,6-DIHYDRO-7H-BENZ[H]-IMIDAZ[4,5-F]ISOQUINOLIN-7-ONE"
    experimentalDB071615-phenyl-1H-indazol-3-amine
    experimentalDB071624-(3-amino-1H-indazol-5-yl)-N-tert-butylbenzenesulfonamide
    experimentalDB080674-[(2-{4-[(CYCLOPROPYLCARBAMOYL)AMINO]-1H-PYRAZOL-3-YL}-1H-BENZIMIDAZOL-6-YL)METHYL]MORPHOLIN-4-IUM
    experimentalDB08183"3-{(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}-3-oxopropanenitrile"