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: SCN5A

    Description: "sodium channel, voltage-gated, type V, alpha subunit"

    Entrez Gene ID: 6331

    SwissProt Acc Number: Q14524

    RefSeq: NM_000335

    It was suspected to be CHD related:

    .."Two novel genetic variants, one in the cardiac sodium channel gene SCN5A and another at 4q25 previously associated with atrial fibrillation, are associated with SCD."..

    From PMID: 22844511, in Journal PLoS One , 2012


    References

    There were 11 potential papers with SCN5A and CHD.

    PMIDTitleJournalsDetails
    24068186 Role of genetic polymorphisms of ion channels in the pathophysiology of coronary microvascular dysfunction and ischemic heart disease.Basic research in cardiologyMore Details
    22844511 Common genetic variants associated with sudden cardiac death: the FinSCDgen study.PloS oneMore Details
    21410720 Mutation analysis ion channel genes ventricular fibrillation survivors with coronary artery disease.Pacing and clinical electrophysiology : PACEMore Details
    20102864 "Etiology of sudden death in the community: results of anatomical, metabolic, and genetic evaluation."American heart journalMore Details
    21179275 Remodeling of ion channel expression in patients with chronic atrial fibrillation and mitral valvular heart disease.The Korean journal of internal medicineMore Details
    20129298 Atrial electrophysiological and structural remodeling in high-risk patients with Brugada syndrome: assessment with electrophysiology and echocardiography.Heart rhythm : the official journal of the Heart Rhythm SocietyMore Details
    19103989 "Epicardial border zone overexpression of skeletal muscle sodium channel SkM1 normalizes activation, preserves conduction, and suppresses ventricular arrhythmia: an in silico, in vivo, in vitro study."CirculationMore Details
    18674739 "Effect of common KCNE1 and SCN5A ion channel gene variants on T-wave alternans, a marker of cardiac repolarization, during clinical exercise stress test: the Finnish Cardiovascular Study."Translational research : the journal of laboratory and clinical medicineMore Details
    16731473 Allelic variants of SCN5A and risk of sudden cardiac arrest in patients with coronary artery disease.Heart rhythm : the official journal of the Heart Rhythm SocietyMore Details
    15851319 QT interval is a heritable quantitative trait with evidence of linkage to chromosome 3 in a genome-wide linkage analysis: The Framingham Heart Study.Heart rhythm : the official journal of the Heart Rhythm SocietyMore Details
    16344400 Cardiac histological substrate in patients with clinical phenotype of Brugada syndrome.CirculationMore Details

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



    PPI interactions

    There were totally 18 unique genes interacted with SCN5A. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SNTB2 Affinity Capture-Western9412493|9412493 No
    SNTA1 Affinity Capture-Western9412493 No
    SNTB1 Affinity Capture-Western9412493|9412493 No
    UBC Affinity Capture-Western15217910|15548568 No
    NEDD4 Reconstituted Complex15217910 No
    CALM1 Two-hybrid11807557 No
    WWP2 Reconstituted Complex15548568 No
    CBL in vivo8621719 No
    SCN5A in vitro16637659 CHD related
    DLG1 in vitro16637659 No
    DLG3 in vitro16637659 No
    INADL in vitro16637659 No
    RGS3 in vitro16637659 No
    NEDD4L in vitro;in vivo;yeast 2-hybrid15217910,15548568 No
    SNTG2 in vitro;in vivo;yeast 2-hybrid12429735 No
    DLG2 in vitro16637659 No
    DLG4 in vitro16637659 No
    RGS2 yeast 2-hybrid16169070 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00192IndecainideFor the treatment of life-threatening dysrhythmias and sustained ventricular tachycardia.
    approvedDB00243Ranolazine"For the treatment of chronic angina. It should be used in combination with amlodipine, beta-blockers or nitrates."C01EB18
    approvedDB00252Phenytoin"For the control of generalized tonic-clonic (grand mal) and complex partial (psychomotor, temporal lobe) seizures and prevention and treatment of seizures occurring during or following neurosurgery."N03AB02;N03AB04;N03AB05
    approvedDB00280Disopyramide"For the treatment of documented ventricular arrhythmias, such as sustained ventricular tachycardia, ventricular pre-excitation and cardiac dysrhythmias. It is a Class Ia antiarrhythmic drug."C01BA03
    approvedDB00281LidocaineFor production of local or regional anesthesia by infiltration techniques such as percutaneous injection and intravenous regional anesthesia by peripheral nerve block techniques such as brachial plexus and intercostal and by central neural techniques such as lumbar and caudal epidural blocks.C01BB01;C05AD01;D04AB01;N01BB02;R02AD02;S01HA07;S02DA01;A01AD11
    approvedDB00379Mexiletine"For the treatment of ventricular tachycardia and symptomatic premature ventricular beats, and prevention of ventricular fibrillation."C01BB02
    approvedDB00473Hexylcaine"Used as a local anesthetic for surface application, infiltration or nerve block"
    approvedDB00527DibucaineFor production of local or regional anesthesia by infiltration techniques such as percutaneous injection and intravenous regional anesthesia by peripheral nerve block techniques such as brachial plexus and intercostal and by central neural techniques such as lumbar and caudal epidural blocks.C05AD04;D04AB02;N01BB06;S02DA04;S01HA06
    approvedDB00532MephenytoinFor the treatment of refractory partial epilepsy.N03AB04
    approvedDB00564CarbamazepineFor the treatment of epilepsy and pain associated with true trigeminal neuralgia.N03AF01
    approvedDB00661Verapamil"For the treatment of hypertension, angina, and cluster headache prophylaxis."C08DA01
    approvedDB00680MoricizineUsed to treat irregular heartbeats (arrhythmias) and maintain a normal heart rate.C01BG01
    approvedDB00740Riluzole"For the treatment of amyotrophic lateral sclerosis (ALS, Lou Gehrig's Disease)"N07XX02
    approvedDB00750PrilocaineUsed as a local anaesthetic and is often used in dentistry.N01BB04
    approvedDB00754EthotoinFor the control of tonic-clonic (grand mal) and complex partial (psychomotor) seizures.N03AB01
    approvedDB00776OxcarbazepineFor use as monotherapy or adjunctive therapy in the treatment of partial seizures in adults with epilepsy and as adjunctive therapy in the treatment of partial seizures in children ages 4-16 with epilepsy.N03AF02
    approvedDB00868BenzonatateFor the symptomatic relief of cough. Has also been applied locally in the oral cavity in adults by releasing the drug from the liquid-filled capsules to provide oropharyngeal anesthesia for conscious intubation.R05DB01
    illicit;approvedDB00907Cocaine"For the introduction of local (topical) anesthesia of accessible mucous membranes of the oral, laryngeal and nasal cavities."N01BC01;R02AD03;S01HA01;S02DA02
    approvedDB00908QuinidineFor the treatment of ventricular pre-excitation and cardiac dysrhythmiasC01BA01
    approvedDB00909ZonisamideFor use as adjunctive treatment of partial seizures in adults with epilepsy.N03AX15
    approvedDB01035ProcainamideFor the treatment of life-threatening ventricular arrhythmias.C01BA02
    approvedDB01056Tocainide"For the treatment of documented ventricular arrhythmias, such as sustained ventricular tachycardia, that, in the judgment of the physician, are life-threatening."C01BB03
    approvedDB01182Propafenone"Used to prolong the time to recurrence of paroxysmal atrial fibrillation/flutter (PAF) associated with disabling symptoms in patients without structural heart disease. Also used for the treatment of life-threatening documented ventricular arrhythmias, such as sustained ventricular tachycardia."C01BC03
    approvedDB01195Flecainide"Flecainide is is a class Ic antiarrhythmic agent and as such, it is used for the prevention of paroxysmal supraventricular tachycardias (PSVT), including atrioventricular nodal reentrant tachycardia, atrioventricular reentrant tachycardia and other supraventricular tachycardias of unspecified mechanism associated with disablin."C01BC04
    approved;withdrawnDB01228Encainide"Encainide is a class Ic antiarrhythmic agent which was used for management of irregular heartbeats, such as atrial fibrillation, atrial flutter, ventricular tachycardia, and ventricular fibrillation. "C01BC08
    approvedDB01320Fosphenytoin"For the control of generalized convulsive status epilepticus and prevention and treatment of seizures occurring during neurosurgery. It can also be substituted, short-term, for oral phenytoin."N03AB05
    approvedDB01346Quinidine barbiturate
    approvedDB01429AprindineC01BB04