Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 KCNC2
Basic gene info.Gene symbolKCNC2
Gene namepotassium voltage-gated channel, Shaw-related subfamily, member 2
SynonymsKV3.2
CytomapUCSC genome browser: 12q14.1
Genomic locationchr12 :75433895-75603511
Type of geneprotein-coding
RefGenesNM_001260497.1,
NM_001260498.1,NM_001260499.1,NM_139136.3,NM_139137.3,
NM_153748.2,
Ensembl idENSG00000166006
Descriptionpotassium voltage-gated channel subfamily C member 2voltage-gated potassium channel Kv3.2
Modification date20141207
dbXrefs MIM : 176256
HGNC : HGNC
Ensembl : ENSG00000166006
HPRD : 08883
Vega : OTTHUMG00000169717
ProteinUniProt: Q96PR1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KCNC2
BioGPS: 3747
Gene Expression Atlas: ENSG00000166006
The Human Protein Atlas: ENSG00000166006
PathwayNCI Pathway Interaction Database: KCNC2
KEGG: KCNC2
REACTOME: KCNC2
ConsensusPathDB
Pathway Commons: KCNC2
MetabolismMetaCyc: KCNC2
HUMANCyc: KCNC2
RegulationEnsembl's Regulation: ENSG00000166006
miRBase: chr12 :75,433,895-75,603,511
TargetScan: NM_001260497
cisRED: ENSG00000166006
ContextiHOP: KCNC2
cancer metabolism search in PubMed: KCNC2
UCL Cancer Institute: KCNC2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for KCNC2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: KCNC2
Familial Cancer Database: KCNC2
* 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 176256; gene.
Orphanet
DiseaseKEGG Disease: KCNC2
MedGen: KCNC2 (Human Medical Genetics with Condition)
ClinVar: KCNC2
PhenotypeMGI: KCNC2 (International Mouse Phenotyping Consortium)
PhenomicDB: KCNC2

Mutations for KCNC2
* 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
ovaryKCNC2chr127547561275475632KCNC2chr127547586375475883
ovaryKCNC2chr127550670675506726LINC00535chr89449797694497996
ovaryKCNC2chr127557738775577407KCNC2chr127557744275577462
pancreasKCNC2chr127548541575485435TTC28chr222906542529065445
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 KCNC2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample72      3      11
GAIN (# sample)62      3      11
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=99)
Stat. for Synonymous SNVs
(# total SNVs=31)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=1)

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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
chr12:75444552-75444552p.N411N4
chr12:75444659-75444659p.R376*4
chr12:75444468-75444468p.G439G4
chr12:75444475-75444475p.T437I3
chr12:75444191-75444191p.L532I2
chr12:75601145-75601145p.R207C2
chr12:75444891-75444891p.L298F2
chr12:75445018-75445018p.I256T2
chr12:75444575-75444575p.E404K2
chr12:75601185-75601185p.E193D2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 194 7 12 2172 11816 11
# mutation13 184 7 12 2272 11915 14
nonsynonymous SNV12 143 2 11 1752  115 9
synonymous SNV 1 41 5  1 52  1810 5
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
chr12:75444552p.N411N,KCNC23
chr12:75444468p.G75G,KCNC22
chr12:75444506p.L298F,KCNC22
chr12:75601539p.T283T,KCNC22
chr12:75444891p.G439G,KCNC22
chr12:75601404p.G427R,KCNC22
chr12:75444936p.T120T,KCNC22
chr12:75434972p.E252K,KCNC21
chr12:75444255p.Y599H1
chr12:75444758p.T120N,KCNC21

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 KCNC2 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 KCNC2

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

CCDC64,DCLK1,DNAJC12,FAM134B,GPC5,GPER1,GRAMD1A,
KCNC2,KDM4B,LMX1B,MADD,MS4A8,MYT1,NLRP8,
SLC8A2,SPO11,SYN1,SYP,THSD4,TRIM36,ZNF587
A1CF,ANKFN1,SMCO3,C8B,FGL1,HABP2,HNF1A,
HNF4G,IGFL2,KCNC2,MIA2,MMP16,NKAIN3,PROC,
SERPINA4,SH3GL3,TMED6,TMEM130,TMEM59L,TTLL6,UGT2B15

ACSS3,CAMKV,GRM4,KCNC1,KCNC2,KCNH6,KLRF1,
LOC254559,MARCH11,OR6F1,PCA3,PRMT8,RNF113B,RPRML,
RSPO4,SCG3,SLC22A1,SLC6A15,SNAP25,TRIM63,ZNF738
FNDC9,CALY,CEND1,CHRNA3,CTNNA2,ELAVL4,GAP43,
GNG3,KCNC2,LRRC4C,MAL,MYOT,OLFM3,PAQR6,
PHOX2B,RTN1,SULT4A1,SYNGR3,TMEM59L,TSPAN11,UCHL1
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 KCNC2


There's no related Drug.
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Cross referenced IDs for KCNC2
* 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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