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.

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  • 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.

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  • 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: PPARG

    Description: peroxisome proliferator-activated receptor gamma

    Entrez Gene ID: 5468

    SwissProt Acc Number: P37231

    RefSeq: NM_005037

    It was suspected to be CHD related:

    .."Peroxisome proliferator-activated receptor gamma (PPAR gamma) plays an important role in lipid metabolism, insulin sensitivity, atherogenesis, and immune regulation."..

    From PMID: 14616762, in Journal Clin Genet. , 2003


    References

    There were 14 potential papers with PPARG and CHD.

    PMIDTitleJournalsDetails
    23583468 "Different effects of PPARA, PPARG and ApoE SNPs on serum lipids in patients with coronary heart disease based on the presence of diabetes."GeneMore Details
    23065280 The effect of PPARG gene polymorphisms on the risk of coronary heart disease: a meta-analysis.Molecular biology reportsMore Details
    23468932 Integrative bioinformatics analysis of genomic and proteomic approaches to understand the transcriptional regulatory program in coronary artery disease pathways.PloS oneMore Details
    22515931 Association of the PPARG Pro12Ala polymorphism with type 2 diabetes and incident coronary heart disease in a Hong Kong Chinese population.Diabetes research and clinical practiceMore Details
    22987045 "The meta-analysis of the association of PPARG P12A, C161T polymorphism and coronary heart disease."Wiener klinische WochenschriftMore Details
    22990020 Genome-wide association study for circulating levels of PAI-1 provides novel insights into its regulation.BloodMore Details
    21833536 Effects of the PPARG P12A and C161T gene variants on serum lipids in coronary heart disease patients with and without Type 2 diabetes.Molecular and cellular biochemistryMore Details
    21036322 Genetics of adipose tissue biology.Progress in molecular biology and translational scienceMore Details
    19955787 Gene-environment interactions in obesity.Forum of nutritionMore Details
    19543210 PPARG genotype accounts for part of individual variation in body weight reduction in response to calorie restriction."Obesity (Silver Spring, Md.)"More Details
    19117570 PPARgamma promoter polymorphisms and acute coronary syndrome.AtherosclerosisMore Details
    20016803 Peroxisome proliferator-activated receptor gamma polymorphisms and coronary heart disease.PPAR researchMore Details
    18781598 Reassessing the cardiovascular risks and benefits of thiazolidinediones.Clinical cardiologyMore Details
    17999084 Relationship between two sequence variations in the gene for peroxisome proliferator-activated receptor-gamma and plasma homocysteine concentration. Health in men study.Human geneticsMore Details

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



    PPI interactions

    There were totally 84 unique genes interacted with PPARG. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    NCOA4 Two-hybrid10347167|10347167 No
    PPARGC1A Reconstituted Complex14636573|19631645 CHD related
    HDAC3 Reconstituted Complex12943985|12479814|12479814 CHD related
    HDAC4 Reconstituted Complex12943985 CHD related
    RB1 Affinity Capture-Western12479814|12479814 CHD related
    FABP1 Two-hybrid11226238|11226238 No
    NR0B2 Affinity Capture-Western11696534|11696534 No
    NRIP1 Reconstituted Complex9626662|11500849 No
    NFE2L2 Reconstituted Complex10930400|10930400 CHD related
    CREBBP Reconstituted Complex10848596 No
    NCOA2 Two-hybrid10944516|10944516|11500849 No
    MED1 Two-hybrid10944516|10944516|11500849|11027271|10037764|17468099 No
    NCOA3 Two-hybrid10944516|10944516|11500849|11027271 No
    ZBTB5 Two-hybrid20211142 No
    NR2E3 Two-hybrid20211142 No
    MAFF Two-hybrid20211142 No
    ZBTB20 Two-hybrid20211142 No
    ZBTB3 Two-hybrid20211142 No
    ZNF496 Two-hybrid20211142 No
    ZBTB9 Two-hybrid20211142 No
    ZSCAN1 Two-hybrid20211142 No
    PIAS1 Affinity Capture-Western16127449 No
    NCOR2 Co-localization15681609 No
    HMGA1 Reconstituted Complex18310298|10428834 CHD related
    SP1 Reconstituted Complex18310298|20360975|22282354 No
    TFAP2A Reconstituted Complex18310298 No
    CEBPB Reconstituted Complex18310298 No
    ZNHIT3 FRET11500849 No
    TRIP4 FRET11500849 No
    JMJD1C FRET11500849 No
    NFKBIB FRET11500849 No
    SERPINH1 FRET11500849 No
    NCOA1 FRET11500849|11027271|9121466|9041124,10848596 No
    TRIM24 FRET11500849 No
    GRIP1 Reconstituted Complex11027271 No
    KAT5 Reconstituted Complex18096664 No
    CHD7 Reconstituted Complex17952062 No
    SETDB1 Reconstituted Complex17952062 No
    HDAC1 Reconstituted Complex16407282 CHD related
    UBC Affinity Capture-Western19951908 No
    COPS5 Two-hybrid15604093|15604093 No
    FHOD1 Two-hybrid15604093 No
    KIF1A Two-hybrid15604093|15604093 No
    SUMO1 Affinity Capture-Western19625650|15507114 No
    ESR1 Far Western9121466 CHD related
    ESR2 Far Western9121466 CHD related
    KDM4C Affinity Capture-Western21637537 No
    TNP1 Two-hybrid21967852 No
    KCTD13 Two-hybrid16239304 No
    APP Reconstituted Complex21832049 No
    RXRG in vivo12615696 No
    PPARG in vitro10339548,11831892,12672231,9744270 CHD related
    - in vitro;yeast 2-hybrid16239304 No
    FOXO1 in vitro;yeast 2-hybrid12966085 CHD related
    RANBP9 yeast 2-hybrid15604093 No
    GADD45G Reconstituted Complex10872826|10872826 No
    Gadd45b Reconstituted Complex10872826 No
    DNTTIP2 Reconstituted Complex15047147|1504714 No
    EP300 Reconstituted Complex12479814|17468099 CHD related
    EDF1 Reconstituted Complex12040021|12040021|12040021 No
    SVIL Two-hybrid11792840 No
    POU1F1 Reconstituted Complex11891224 No
    RXRA Co-purification7838715 CHD related
    MED24 Reconstituted Complex9653119|9653119 No
    MSX2 Two-hybrid20211142 No
    PML Two-hybrid20211142 No
    NCOR1 Two-hybrid16127449|15681609|17468099|11877444,11903058,15604093 No
    LRIF1 Reconstituted Complex17455211 No
    NLK Co-purification17952062|17952062 No
    MECP2 Affinity Capture-RNA21151932 No
    EZH2 Affinity Capture-RNA21151932 No
    NCOA6 Two-hybrid15604093|10788465,15604093 No
    NR0B1 Two-hybrid15604093|15604093 No
    RXRB Two-hybrid15604093|15604093 No
    ROBO4 Reconstituted Complex14761960 No
    KLF4 Affinity Capture-Western22282354|22282354 No
    RAD54L2 Reconstituted Complex19692572 No
    ANP32A Reconstituted Complex15308690 No
    MAPK1 in vitro;in vivo9030579 CHD related
    MAPK8 in vitro;in vivo9030579 CHD related
    BRD8 yeast 2-hybrid10517671 No
    SMARCD3 in vitro14701856 No
    CNOT1 yeast 2-hybrid16778766 No
    SYT1 in vitro;yeast 2-hybrid16143103 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00159Icosapent"EPA can be used for lowering elevated triglycerides in those who are hyperglyceridemic. In addition, EPA may play a therapeutic role in patients with cystic fibrosis by reducing disease severity and may play a similar role in type 2 diabetics in slowing the progression of diabetic nephropathy."C10AX06
    withdrawnDB00197Troglitazone"For the treatment of Type II diabetes mellitus. It is used alone or in combination with a sulfonylurea, metformin, or insulin as an adjunct to diet and exercise."A10BG01
    approvedDB00244MesalazineFor the treatment of active ulcerative proctitis.A07EC02
    approvedDB00328Indomethacin"For moderate to severe rheumatoid arthritis including acute flares of chronic disease, ankylosing spondylitis, osteoarthritis, acute painful shoulder (bursitis and/or tendinitis) and acute gouty arthritis."M01AB01;C01EB03
    approvedDB00412RosiglitazoneFor the treatment of Type II diabetes mellitusA10BG02
    approvedDB00731NateglinideFor the treatment of non-insulin dependent-diabetes mellitus in conjunction with diet and exercise.A10BX03
    approvedDB00795SulfasalazineFor the treatment of Crohn's disease and rheumatoid arthritis as a second-line agent.A07EC01
    approvedDB00912RepaglinideFor the treatment of non-insulin dependent-diabetes mellitus in conjunction with diet and exercise. A10BX02
    approvedDB00966Telmisartan"Used alone or in combination with other classes of antihypertensives for the treatment of hypertension. Also used in the treatment of diabetic nephropathy in hypertensive patients with type 2 diabetes mellitus, as well as the treatment of congestive heart failure (only in patients who cannot tolerate ACE inhibitors)."C09CA07
    approvedDB01014BalsalazideFor the treatment of mildly to moderately active ulcerative colitis.A07EC04
    approvedDB01067Glipizide"For use as an adjunct to diet for the control of hyperglycemia and its associated symptomatology in patients with non-insulin-dependent diabetes mellitus (NIDDM; type II), formerly known as maturity-onset diabetes, after an adequate trial of dietary therapy has proved unsatisfactory."A10BB07
    approvedDB01132PioglitazoneTreatment of Type II diabetes mellitusA10BG03
    approvedDB01252MitiglinideFor the treatment of type 2 diabetes.A10BX08
    approvedDB01393Bezafibrate"For the treatment of primary hyperlipidaemia types IIa, IIb, III, IV and V (Fredrickson classification) corresponding to groups I, II and III of the European Atherosclerosis Society guidelines - when diet alone or improvements in lifestyle such as increased exercise or weight reduction do not lead to an adequate response. Also for the treatment of secondary hyperlipidaemias, e.g. severe hypertriglyceridemias, when sufficient improvement does not occur after correction of the underlying disorder (e.g. diabetes mellitus)."C10AB02
    experimentalDB04270(S)-3-(4-(2-Carbazol-9-Yl-Ethoxy)-Phenyl)-2-Ethoxy-Propionic Acid
    experimentalDB046892-{5-[3-(6-BENZOYL-1-PROPYLNAPHTHALEN-2-YLOXY)PROPOXY]INDOL-1-YL}ETHANOIC ACID
    experimentalDB06908"(2S)-3-(1-{[2-(2-CHLOROPHENYL)-5-METHYL-1,3-OXAZOL-4-YL]METHYL}-1H-INDOL-5-YL)-2-ETHOXYPROPANOIC ACID"
    experimentalDB06926"(9Z,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid"
    experimentalDB070532-{5-[3-(7-PROPYL-3-TRIFLUOROMETHYLBENZO[D]ISOXAZOL-6-YLOXY)PROPOXY]INDOL-1-YL}ETHANOIC ACID
    experimentalDB07111"(4S,5E,7Z,10Z,13Z,16Z,19Z)-4-hydroxydocosa-5,7,10,13,16,19-hexaenoic acid"
    experimentalDB07172"(5R,6E,8Z,11Z,14Z,17Z)-5-hydroxyicosa-6,8,11,14,17-pentaenoic acid"
    experimentalDB07208"(8E,10S,12Z)-10-hydroxy-6-oxooctadeca-8,12-dienoic acid"
    experimentalDB07209"(8R,9Z,12Z)-8-hydroxy-6-oxooctadeca-9,12-dienoic acid"
    experimentalDB07302"(9S,10E,12Z)-9-hydroxyoctadeca-10,12-dienoic acid"
    experimentalDB07509difluoro(5-{2-[(5-octyl-1H-pyrrol-2-yl-kappaN)methylidene]-2H-pyrrol-5-yl-kappaN}pentanoato)boron
    experimentalDB07675(2S)-2-ETHOXY-3-{4-[2-(10H-PHENOXAZIN-10-YL)ETHOXY]PHENYL}PROPANOIC ACID
    experimentalDB077233-(5-methoxy-1H-indol-3-yl)propanoic acid
    experimentalDB077243-{5-methoxy-1-[(4-methoxyphenyl)sulfonyl]-1H-indol-3-yl}propanoic acid
    experimentalDB07842(2S)-2-(4-ethylphenoxy)-3-phenylpropanoic acid
    experimentalDB078632-chloro-5-nitro-N-phenylbenzamide
    experimentalDB08121(2S)-2-(biphenyl-4-yloxy)-3-phenylpropanoic acid
    experimentalDB083023-[5-(2-nitropent-1-en-1-yl)furan-2-yl]benzoic acid
    experimentalDB08402"2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID"
    experimentalDB08435"(5E,14E)-11-oxoprosta-5,9,12,14-tetraen-1-oic acid"
    experimentalDB08483"(2S)-2-methoxy-3-{4-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl)ethoxy]-1-benzothiophen-7-yl}propanoic acid"
    experimentalDB085603-FLUORO-N-[1-(4-FLUOROPHENYL)-3-(2-THIENYL)-1H-PYRAZOL-5-YL]BENZENESULFONAMIDE
    experimentalDB08760(2S)-2-(4-chlorophenoxy)-3-phenylpropanoic acid