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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CA4 |
Basic gene info. | Gene symbol | CA4 |
Gene name | carbonic anhydrase IV | |
Synonyms | CAIV|Car4|RP17 | |
Cytomap | UCSC genome browser: 17q23 | |
Genomic location | chr17 :58227301-58236906 | |
Type of gene | protein-coding | |
RefGenes | NM_000717.3, | |
Ensembl id | ENSG00000167434 | |
Description | CA-IVcarbonate dehydratase IVcarbonic anhydrase 4carbonic dehydratase IV | |
Modification date | 20141219 | |
dbXrefs | MIM : 114760 | |
HGNC : HGNC | ||
Ensembl : ENSG00000167434 | ||
HPRD : 00261 | ||
Vega : OTTHUMG00000179987 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_CA4 | |
BioGPS: 762 | ||
Gene Expression Atlas: ENSG00000167434 | ||
The Human Protein Atlas: ENSG00000167434 | ||
Pathway | NCI Pathway Interaction Database: CA4 | |
KEGG: CA4 | ||
REACTOME: CA4 | ||
ConsensusPathDB | ||
Pathway Commons: CA4 | ||
Metabolism | MetaCyc: CA4 | |
HUMANCyc: CA4 | ||
Regulation | Ensembl's Regulation: ENSG00000167434 | |
miRBase: chr17 :58,227,301-58,236,906 | ||
TargetScan: NM_000717 | ||
cisRED: ENSG00000167434 | ||
Context | iHOP: CA4 | |
cancer metabolism search in PubMed: CA4 | ||
UCL Cancer Institute: CA4 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for CA4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: CA4 |
Familial Cancer Database: CA4 |
* This gene is included in those cancer gene databases. |
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 | |
KEGG_NITROGEN_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: CA4 |
MedGen: CA4 (Human Medical Genetics with Condition) | |
ClinVar: CA4 | |
Phenotype | MGI: CA4 (International Mouse Phenotyping Consortium) |
PhenomicDB: CA4 |
Mutations for CA4 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CA4 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 |
Other DBs for Structural Variants |
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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 |   |   |   | 1 |   |   |   |   | 1 |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   | 1 |   |   |   |   | 1 |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=16) | (# total SNVs=10) |
(# total SNVs=1) | (# total SNVs=0) |
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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 |
chr17:58234054-58234054 | p.T82T | 2 |
chr17:58234066-58234066 | p.N86N | 2 |
chr17:58232704-58232704 | p.E30K | 1 |
chr17:58235707-58235708 | p.R215I | 1 |
chr17:58234039-58234039 | p.K77K | 1 |
chr17:58234891-58234891 | p.K124K | 1 |
chr17:58233921-58233921 | p.V38A | 1 |
chr17:58235758-58235758 | p.K232R | 1 |
chr17:58234905-58234905 | p.S129I | 1 |
chr17:58233923-58233923 | p.P39A | 1 |
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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 | 1 | 2 |   | 5 |   |   | 4 |   | 1 |   |   | 4 | 1 | 1 |   |   | 7 | 4 |   | 1 |
# mutation | 1 | 2 |   | 5 |   |   | 4 |   | 1 |   |   | 4 | 1 | 1 |   |   | 7 | 4 |   | 1 |
nonsynonymous SNV | 1 | 1 |   | 3 |   |   | 4 |   |   |   |   | 3 | 1 | 1 |   |   | 4 | 3 |   | 1 |
synonymous SNV |   | 1 |   | 2 |   |   |   |   | 1 |   |   | 1 |   |   |   |   | 3 | 1 |   |   |
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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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 |
chr17:58233921 | p.E30K | 1 |
chr17:58234824 | p.K124K | 1 |
chr17:58235657 | p.V38A | 1 |
chr17:58233923 | p.S129I | 1 |
chr17:58234830 | p.P39A | 1 |
chr17:58235697 | p.G148E | 1 |
chr17:58233927 | p.V40A | 1 |
chr17:58234865 | p.S150S | 1 |
chr17:58235751 | p.V40V | 1 |
chr17:58233928 | p.V170G | 1 |
Other DBs for Point Mutations |
Copy Number for CA4 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 CA4 |
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. |
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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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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 |
AQP7,AQP7P1,ATOH8,BTNL9,C14orf180,CA4,CD300LG, CLDN5,CRHBP,GLYAT,GPIHBP1,GPR146,HSD17B13,KCNIP2, LEP,NPR1,PDE2A,PLIN1,RDH5,SDPR,SLC22A12 | ABLIM3,BTNL9,CA4,CD300LG,EHD2,GNAZ,GPER1, GPIHBP1,GPR146,HOXB7,INPP5K,LOC158376,NRN1,PALM, PTH1R,RBP7,RRAS,ST6GALNAC6,TCF15,VEGFB,VTI1B | ||||
ASPG,BTNL3,CA2,CA4,CASP5,CDKN2B-AS1,CEACAM7, CLCA4,GUCA2A,GUCA2B,MS4A12,SLC51B,OTOP2,SCNN1B, SEPP1,SLC25A34,SLC26A3,SLC30A10,SLC6A19,TMIGD1,TRIM40 | AMACR,ATP1B3,CNPPD1,CA4,CAPN2,CEACAM7,CLCN2, ABHD17C,GBA,GTPBP2,LITAF,MGLL,P2RX4,PEX26, PPARG,PRR15,SGK2,SLC26A3,TJP3,TMEM8A,TSPAN1 |
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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for CA4 |
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. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00232 | carbonic anhydrase IV | approved | Methyclothiazide | ||
DB00273 | carbonic anhydrase IV | approved; investigational | Topiramate | ||
DB00311 | carbonic anhydrase IV | approved | Ethoxzolamide | ||
DB00436 | carbonic anhydrase IV | approved | Bendroflumethiazide | ||
DB00562 | carbonic anhydrase IV | approved | Benzthiazide | ||
DB00606 | carbonic anhydrase IV | approved | Cyclothiazide | ||
DB00703 | carbonic anhydrase IV | approved | Methazolamide | ||
DB00774 | carbonic anhydrase IV | approved | Hydroflumethiazide | ||
DB00819 | carbonic anhydrase IV | approved | Acetazolamide | ||
DB00869 | carbonic anhydrase IV | approved | Dorzolamide | ||
DB00880 | carbonic anhydrase IV | approved | Chlorothiazide | ||
DB00909 | carbonic anhydrase IV | approved; investigational | Zonisamide | ||
DB00999 | carbonic anhydrase IV | approved | Hydrochlorothiazide | ||
DB01021 | carbonic anhydrase IV | approved | Trichlormethiazide | ||
DB01144 | carbonic anhydrase IV | approved | Dichlorphenamide | ||
DB01194 | carbonic anhydrase IV | approved | Brinzolamide |
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Cross referenced IDs for CA4 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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