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: CACNA1C

    Description: "calcium channel, voltage-dependent, L type, alpha 1C subunit"

    Entrez Gene ID: 775

    SwissProt Acc Number: Q13936

    RefSeq: NM_000719

    It was suspected to be CHD related:

    ..Variation in CACNA1C is associated with treatment response among hypertensive patients with stable coronary artery disease...

    From PMID: 20031608, in Journal Circ Cardiovasc Genet , 2009


    References

    There were 2 potential papers with CACNA1C and CHD.

    PMIDTitleJournalsDetails
    21658281 GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease.BMC cardiovascular disordersMore Details
    20031608 "CACNA1C gene polymorphisms, cardiovascular disease outcomes, and treatment response."Circulation. Cardiovascular geneticsMore Details

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



    PPI interactions

    There were totally 18 unique genes interacted with CACNA1C. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    RYR2 Reconstituted Complex11576544 CHD related
    SRI Reconstituted Complex9668070 No
    HDAC4 Reconstituted Complex21464227 CHD related
    VCP Affinity Capture-Western21186355 No
    DERL1 Affinity Capture-Western21186355 No
    UBC Affinity Capture-Western21186355 No
    TRIM13 Affinity Capture-Western21186355 No
    COPS5 Two-hybrid16483597 No
    GNB1 yeast 2-hybrid15953418 No
    PCBD1 Two-hybrid11461190 No
    CACNB3 Co-crystal Structure15170217|15170217 No
    CABP1 Reconstituted Complex15140941|15140941 No
    SIRT1 Affinity Capture-MS19343720 CHD related
    CUL1 Affinity Capture-MS21145461 No
    CAND1 Affinity Capture-MS21145461 No
    PRKACA in vitro;in vivo8612821,9247274,8664319 CHD related
    PPM1A in vitro;in vivo15728831 No
    RIMS1 in vitro11438519 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00270IsradipineFor the management of mild to moderate essential hypertension. It may be used alone or concurrently with thiazide-type diuretics.C08CA03
    approvedDB00308IbutilideIndicated for the rapid conversion of atrial fibrillation or atrial flutter of recent onset to sinus rhythm.C01BD05
    approvedDB00381AmlodipineFor the treatment of hypertension and chronic stable angina.C08CA01
    approvedDB00393NimodipineFor use as an adjunct to improve neurologic outcome following subarachnoid hemorrhage (SAH) from ruptured intracranial berry aneurysms by reducing the incidence and severity of ischemic deficits.C08CA06
    approvedDB00401NisoldipineFor the treatment of hypertension. It may be used alone or in combination with other antihypertensive agents.C08CA07
    approvedDB00568Cinnarizine"For the treatment of vertigo/meniere's disease, nausea and vomiting, motion sickness and also useful for vestibular symptoms of other origins."N07CA02
    approvedDB00622NicardipineUsed for the management of patients with chronic stable angina and for the treatment of hypertension.C08CA04
    approvedDB00653Magnesium Sulfate"Used for immediate control of life-threatening convulsions in the treatment of severe toxemias (pre-eclampsia and eclampsia) of pregnancy and in the treatment of acute nephritis in children. Also indicated for replacement therapy in magnesium deficiency, especially in acute hypomagnesemia accompanied by signs of tetany similar to those of hypocalcemia. Also used in uterine tetany as a myometriat relaxant."A06AD04;A12CC02;B05XA05;D11AX05;V04CC02
    approvedDB00661Verapamil"For the treatment of hypertension, angina, and cluster headache prophylaxis."C08DA01
    approvedDB01023FelodipineFor the treatment of mild to moderate essential hypertension. C08CA02
    approvedDB01054NitrendipineFor the treatment of mild to moderate hypertensionC08CA08
    approvedDB01115Nifedipine"For the management of vasospastic angina, chronic stable angina, hypertension, and Raynaud's phenomenon. May be used as a first line agent for left ventricular hypertrophy and isolated systolic hypertension (long-acting agents). "C08CA05
    experimentalDB01373Calcium"Calcium plays a vital role in the anatomy, physiology and biochemistry of organisms and of the cell, particularly in signal transduction pathways. It is vital in cell signaling, muscular contractions, bone health, and signalling cascades."D11AX03;V03AF04;C05BX01;B02BC08;B01AC08;R01AX01;N02BA15;V03AF03;G04BA03;B05XA07;A01AD11;A12AA03;A11HA31;V08AC10;A12AA11;D03AX04;A12AA06;A11GA01;J04AA03;A12AA12;A12AA30;A06AC08;A12AA02;A12AA05;A12AA09;N07BB02;A07XA03;A12AA07;A12AA10;V03AE01;A02AC01;A12AA04;A02AC02;A12AA08;A12AA01;A12AA20
    withdrawnDB01388MibefradilFor the treatment of angina and high blood pressure.C08CX01
    approvedDB06751DrotaverineUsed in the treatment of functional bowel disorders and alleviating pain in renal colic.A03AD02