Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for CACNA1A
Basic gene info.Gene symbolCACNA1A
Gene namecalcium channel, voltage-dependent, P/Q type, alpha 1A subunit
SynonymsAPCA|BI|CACNL1A4|CAV2.1|EA2|FHM|HPCA|MHP|MHP1|SCA6
CytomapUCSC genome browser: 19p13
Genomic locationchr19 :13317255-13617274
Type of geneprotein-coding
RefGenesNM_000068.3,
NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2,
Ensembl idENSG00000141837
Descriptionbrain calcium channel 1brain calcium channel Icalcium channel, L type, alpha-1 polypeptidevoltage-dependent P/Q-type calcium channel subunit alpha-1Avoltage-gated calcium channel subunit alpha Cav2.1
Modification date20141222
dbXrefs MIM : 601011
HGNC : HGNC
Ensembl : ENSG00000141837
HPRD : 03004
Vega : OTTHUMG00000044590
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CACNA1A
BioGPS: 773
Gene Expression Atlas: ENSG00000141837
The Human Protein Atlas: ENSG00000141837
PathwayNCI Pathway Interaction Database: CACNA1A
KEGG: CACNA1A
REACTOME: CACNA1A
ConsensusPathDB
Pathway Commons: CACNA1A
MetabolismMetaCyc: CACNA1A
HUMANCyc: CACNA1A
RegulationEnsembl's Regulation: ENSG00000141837
miRBase: chr19 :13,317,255-13,617,274
TargetScan: NM_000068
cisRED: ENSG00000141837
ContextiHOP: CACNA1A
cancer metabolism search in PubMed: CACNA1A
UCL Cancer Institute: CACNA1A
Assigned class in ccmGDBC

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Phenotypic Information for CACNA1A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CACNA1A
Familial Cancer Database: CACNA1A
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CACNA1A
MedGen: CACNA1A (Human Medical Genetics with Condition)
ClinVar: CACNA1A
PhenotypeMGI: CACNA1A (International Mouse Phenotyping Consortium)
PhenomicDB: CACNA1A

Mutations for CACNA1A
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastCACNA1Achr191346518313465183CACNA1Achr191357198313571983
ovaryCACNA1Achr191342017913420199AP1M1chr191632683616326856
ovaryCACNA1Achr191357869113578711CACNA1Achr191357925313579273
pancreasCACNA1Achr191331927413319294CACNA1Achr191337921013379230
pancreasCACNA1Achr191333182913332029chr57103188871032088
pancreasCACNA1Achr191334110913341129chr193234317332343193
pancreasCACNA1Achr191337706813377088chr192781209127812111
pancreasCACNA1Achr191340805513408075CACNA1Achr191343830313438323
pancreasCACNA1Achr191341231113412511LOC100506012chr194702054647020746
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CACNA1A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA772930CACNA1A277191331884513319628DNAJC13784233132235269132241832

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample4 14  1 1 9   1  
GAIN (# sample)4 14  1 1 9      
LOSS (# sample)              1  
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=148)
Stat. for Synonymous SNVs
(# total SNVs=61)
Stat. for Deletions
(# total SNVs=12)
Stat. for Insertions
(# total SNVs=3)

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr19:13418659-13418659p.F641F6
chr19:13319693-13319693p.H2219H4
chr19:13470495-13470495p.F301F3
chr19:13365981-13365981p.F1561F3
chr19:13566007-13566007p.L105V3
chr19:13414622-13414622p.V688G2
chr19:13419248-13419248p.R588H2
chr19:13445187-13445187p.?2
chr19:13446675-13446675p.L343fs*102
chr19:13409614-13409614p.G945W2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample716 273 12242126104 25018219
# mutation817 403 13252128114 26224229
nonsynonymous SNV513 281 7232 1893 22716219
synonymous SNV34 132 6 2 11021  358 10
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr19:13418659p.F642F,CACNA1A6
chr19:13365981p.F1562F,CACNA1A4
chr19:13414658p.G260E,CACNA1A2
chr19:13373595p.G851S,CACNA1A2
chr19:13418658p.D643N,CACNA1A2
chr19:13409899p.L1934L,CACNA1A2
chr19:13414674p.P1043H,CACNA1A2
chr19:13414675p.R369W,CACNA1A2
chr19:13363807p.I1505I,CACNA1A2
chr19:13335577p.G677E,CACNA1A2

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for CACNA1A in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for CACNA1A

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

AP1M1,MRGPRG-AS1,COLCA2,C15orf41,C1QL3,BPIFB3,C4BPA,
CACNA1A,CYP7A1,DCAF15,DDX39A,GPR85,MROH2B,KCNB2,
KCNS1,MEIS2,MRGPRG,MUC7,PRTFDC1,SLC25A37,ZSWIM4
C14orf119,C1orf110,C8orf59,CACNA1A,COMMD6,DACT3,DAD1,
DSTN,FAM127B,FAM127C,FKBP1B,FLJ42393,KRTCAP2,LOC285954,
LSM2,MAX,PRAF2,RAC1,SUPT4H1,TMEM60,UBE2Q1

ABCC12,ACTL6B,APLP1,ATP2B2,BTBD17,LINC00588,CACNA1A,
CACNG3,CHST8,CUX2,FEV,HCN4,INSRR,JPH4,
LIN28A,NEUROD2,SEZ6,SSTR2,SYT6,THSD7B,VWA5B2
CACNA1A,CALN1,CELSR1,COL2A1,DSCAML1,AMER3,FEV,
GPR119,HOXD12,INSM1,MARCH4,NKX2-2,PAX3,PYY,
RFX6,RIMBP2,SLC18A1,ST6GAL2,TBX4,TOX2,VWA5B2
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for CACNA1A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00230calcium channel, voltage-dependent, P/Q type, alpha 1A subunitillicit; approved; investigationalPregabalin
DB00661calcium channel, voltage-dependent, P/Q type, alpha 1A subunitapprovedVerapamil
DB00836calcium channel, voltage-dependent, P/Q type, alpha 1A subunitapprovedLoperamide
DB01244calcium channel, voltage-dependent, P/Q type, alpha 1A subunitapprovedBepridil


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Cross referenced IDs for CACNA1A
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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