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| Phenotypic Information (metabolism pathway, cancer, disease, phenome) |
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| Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG |
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| Gene Summary for CACNA1A |
| Basic gene info. | Gene symbol | CACNA1A |
| Gene name | calcium channel, voltage-dependent, P/Q type, alpha 1A subunit | |
| Synonyms | APCA|BI|CACNL1A4|CAV2.1|EA2|FHM|HPCA|MHP|MHP1|SCA6 | |
| Cytomap | UCSC genome browser: 19p13 | |
| Genomic location | chr19 :13317255-13617274 | |
| Type of gene | protein-coding | |
| RefGenes | NM_000068.3, NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2, | |
| Ensembl id | ENSG00000141837 | |
| Description | brain 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 date | 20141222 | |
| dbXrefs | MIM : 601011 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000141837 | ||
| HPRD : 03004 | ||
| Vega : OTTHUMG00000044590 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_CACNA1A | |
| BioGPS: 773 | ||
| Gene Expression Atlas: ENSG00000141837 | ||
| The Human Protein Atlas: ENSG00000141837 | ||
| Pathway | NCI Pathway Interaction Database: CACNA1A | |
| KEGG: CACNA1A | ||
| REACTOME: CACNA1A | ||
| ConsensusPathDB | ||
| Pathway Commons: CACNA1A | ||
| Metabolism | MetaCyc: CACNA1A | |
| HUMANCyc: CACNA1A | ||
| Regulation | Ensembl's Regulation: ENSG00000141837 | |
| miRBase: chr19 :13,317,255-13,617,274 | ||
| TargetScan: NM_000068 | ||
| cisRED: ENSG00000141837 | ||
| Context | iHOP: CACNA1A | |
| cancer metabolism search in PubMed: CACNA1A | ||
| UCL Cancer Institute: CACNA1A | ||
| Assigned class in ccmGDB | C | |
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| Phenotypic Information for CACNA1A(metabolism pathway, cancer, disease, phenome) |
 Cancer Description | |
| Cancer | CGAP: CACNA1A |
| Familial Cancer Database: CACNA1A | |
| * This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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/ |
| Metabolic Pathway Description | |
| REACTOME_INTEGRATION_OF_ENERGY_METABOLISM | |
| 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. |
| Structural Variants in COSMIC: go to COSMIC mutation histogram |
| - Statistics for Tissue and Mutation type | Top |
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| - For Inter-chromosomal Variations |
| * Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
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| - 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'. |
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| Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
| breast | CACNA1A | chr19 | 13465183 | 13465183 | CACNA1A | chr19 | 13571983 | 13571983 |
| ovary | CACNA1A | chr19 | 13420179 | 13420199 | AP1M1 | chr19 | 16326836 | 16326856 |
| ovary | CACNA1A | chr19 | 13578691 | 13578711 | CACNA1A | chr19 | 13579253 | 13579273 |
| pancreas | CACNA1A | chr19 | 13319274 | 13319294 | CACNA1A | chr19 | 13379210 | 13379230 |
| pancreas | CACNA1A | chr19 | 13331829 | 13332029 | chr5 | 71031888 | 71032088 | |
| pancreas | CACNA1A | chr19 | 13341109 | 13341129 | chr19 | 32343173 | 32343193 | |
| pancreas | CACNA1A | chr19 | 13377068 | 13377088 | chr19 | 27812091 | 27812111 | |
| pancreas | CACNA1A | chr19 | 13408055 | 13408075 | CACNA1A | chr19 | 13438303 | 13438323 |
| pancreas | CACNA1A | chr19 | 13412311 | 13412511 | LOC100506012 | chr19 | 47020546 | 47020746 |
| 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) |
| Related fusion transcripts : go to Chitars2.0 |
| * From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CACNA1A related fusion information. |
| ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
| AA772930 | CACNA1A | 2 | 77 | 19 | 13318845 | 13319628 | DNAJC13 | 78 | 423 | 3 | 132235269 | 132241832 | |
| Other DBs for Structural Variants |
| Top |
| Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
| Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
| Total # sample | 4 | 1 | 4 | 1 | 1 | 9 | 1 | |||||||||||||
| GAIN (# sample) | 4 | 1 | 4 | 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) |
| Top |
| SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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: Non-synonymous mutation, 
: Synonymous mutation, Circle size denotes number of samples. |
| Top |
| Somatic Mutation Counts per Tissue in COSMIC data |
| Stat. for Non-Synonymous SNVs (# total SNVs=148) | (# total SNVs=61) |
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(# total SNVs=12) | (# total SNVs=3) |
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| Top |
| Top 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 position | Mutation(aa) | Unique sampleID count |
| chr19:13418659-13418659 | p.F641F | 6 |
| chr19:13319693-13319693 | p.H2219H | 4 |
| chr19:13365981-13365981 | p.F1561F | 3 |
| chr19:13566007-13566007 | p.L105V | 3 |
| chr19:13470495-13470495 | p.F301F | 3 |
| chr19:13428038-13428038 | p.R481R | 2 |
| chr19:13397337-13397338 | p.L1178fs*38 | 2 |
| chr19:13409696-13409696 | p.E917D | 2 |
| chr19:13418632-13418632 | p.F650F | 2 |
| chr19:13423526-13423526 | p.T542M | 2 |
| Top |
| SNV Counts per Each Loci in TCGA data |
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| Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
| # sample | 7 | 16 | 27 | 3 | 12 | 2 | 4 | 2 | 1 | 26 | 10 | 4 | 2 | 50 | 18 | 2 | 19 | |||
| # mutation | 8 | 17 | 40 | 3 | 13 | 2 | 5 | 2 | 1 | 28 | 11 | 4 | 2 | 62 | 24 | 2 | 29 | |||
| nonsynonymous SNV | 5 | 13 | 28 | 1 | 7 | 2 | 3 | 2 | 18 | 9 | 3 | 2 | 27 | 16 | 2 | 19 | ||||
| synonymous SNV | 3 | 4 | 13 | 2 | 6 | 2 | 1 | 10 | 2 | 1 | 35 | 8 | 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]) |
| Top |
| Top 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 Position | Mutation(aa) | Unique sampleID count |
| chr19:13418659 | p.F642F,CACNA1A | 6 |
| chr19:13365981 | p.F1562F,CACNA1A | 4 |
| chr19:13365963 | p.G677E,CACNA1A | 2 |
| chr19:13339571 | p.R1349W,CACNA1A | 2 |
| chr19:13414691 | p.E672K,CACNA1A | 2 |
| chr19:13387897 | p.L1623L,CACNA1A | 2 |
| chr19:13418631 | p.N671N,CACNA1A | 2 |
| chr19:13418632 | p.R1880W,CACNA1A | 2 |
| chr19:13397745 | p.G667G,CACNA1A | 2 |
| chr19:13325357 | p.F301F,CACNA1A | 2 |
| Other DBs for Point Mutations |
| Copy 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. |
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| 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] |
| Top |
| Gene Expression for CACNA1A |
| Gene 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. |
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| Differential 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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| Top |
| CNV 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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| Top |
| Gene-Gene Network Information |
| Co-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
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| 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 | ||||
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| 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 |
| Co-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
| Top |
| Interacting Genes (from Pathway Commons) |
: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID
| Top |
| Pharmacological Information for CACNA1A |
| Cross-referenced pharmacological DB IDs from Uniprot |
| DB Category | DB Name | DB's ID and Url link |
| Drug-Gene Interaction Network |
| * Gene Centered Interaction Network. |
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| * Drug Centered Interaction Network. |
| DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
| DB00230 | calcium channel, voltage-dependent, P/Q type, alpha 1A subunit | illicit; approved; investigational | Pregabalin |  |  |
| DB00661 | calcium channel, voltage-dependent, P/Q type, alpha 1A subunit | approved | Verapamil |  |  |
| DB00836 | calcium channel, voltage-dependent, P/Q type, alpha 1A subunit | approved | Loperamide |  |  |
| DB01244 | calcium channel, voltage-dependent, P/Q type, alpha 1A subunit | approved | Bepridil |  |  |
| Top |
| 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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