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 KCNS3
Basic gene info.Gene symbolKCNS3
Gene namepotassium voltage-gated channel, delayed-rectifier, subfamily S, member 3
SynonymsKV9.3
CytomapUCSC genome browser: 2p24
Genomic locationchr2 :18059944-18114225
Type of geneprotein-coding
RefGenesNM_001282428.1,
NM_002252.4,
Ensembl idENSG00000170745
DescriptionShab-related delayed-rectifier K+ channel alpha subunit 3delayed-rectifier K(+) channel alpha subunit 3potassium voltage-gated channel delayed-rectifier protein S3potassium voltage-gated channel subfamily S member 3voltage-gated potassium channel prot
Modification date20141207
dbXrefs MIM : 603888
HGNC : HGNC
Ensembl : ENSG00000170745
HPRD : 04865
Vega : OTTHUMG00000044150
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KCNS3
BioGPS: 3790
Gene Expression Atlas: ENSG00000170745
The Human Protein Atlas: ENSG00000170745
PathwayNCI Pathway Interaction Database: KCNS3
KEGG: KCNS3
REACTOME: KCNS3
ConsensusPathDB
Pathway Commons: KCNS3
MetabolismMetaCyc: KCNS3
HUMANCyc: KCNS3
RegulationEnsembl's Regulation: ENSG00000170745
miRBase: chr2 :18,059,944-18,114,225
TargetScan: NM_001282428
cisRED: ENSG00000170745
ContextiHOP: KCNS3
cancer metabolism search in PubMed: KCNS3
UCL Cancer Institute: KCNS3
Assigned class in ccmGDBC

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Phenotypic Information for KCNS3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: KCNS3
Familial Cancer Database: KCNS3
* 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: KCNS3
MedGen: KCNS3 (Human Medical Genetics with Condition)
ClinVar: KCNS3
PhenotypeMGI: KCNS3 (International Mouse Phenotyping Consortium)
PhenomicDB: KCNS3

Mutations for KCNS3
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryKCNS3chr21808255518082575KCNS3chr21809325118093271
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 KCNS3 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
There's no copy number variation information in COSMIC data for this gene.

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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=10

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=72)
Stat. for Synonymous SNVs
(# total SNVs=21)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr2:18112778-18112778p.R168L5
chr2:18112777-18112777p.R168W5
chr2:18113665-18113665p.D464N4
chr2:18112873-18112873p.V200M3
chr2:18112561-18112561p.V96I3
chr2:18112978-18112978p.G235R3
chr2:18112842-18112842p.I189M2
chr2:18112646-18112646p.R124H2
chr2:18112465-18112465p.D64N2
chr2:18112296-18112296p.F7F2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample121221 4 2  824  137 11
# mutation121161 5 2  824  177 12
nonsynonymous SNV12 101 3 2  424  105 8
synonymous SNV  16  2    4    72 4
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
chr2:18112777p.R168W,KCNS35
chr2:18113665p.D464N,KCNS34
chr2:18112561p.F7F,KCNS32
chr2:18112296p.A228A,KCNS32
chr2:18112959p.S145S,KCNS32
chr2:18112633p.G235R,KCNS32
chr2:18113407p.G235E,KCNS32
chr2:18112978p.D464G,KCNS32
chr2:18112979p.P378S,KCNS32
chr2:18113666p.V96I,KCNS32

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 KCNS3 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 KCNS3

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

ARNT2,SPATA6L,CAPN8,CHRD,CLEC3A,CST5,CYBRD1,
GNG12,IRX2,KCNS3,LRIG1,MIPOL1,PLCL1,RBKS,
SIAE,SLC22A18AS,SLITRK6,THPO,TMEM63C,WT1,ZNF385D
BZW2,LINC00515,VWA7,FAM220A,DEPTOR,DUSP28,GOT2,
KCNS3,LMO7,MAP6D1,P2RY2,PDLIM5,PFN2,PPP1R3C,
PPP2R3A,RBM38,RTN2,SLC20A2,TPM1,TSPYL1,TUBA4A

ALX1,ASAP3,B3GNT9,CYP1A1,FAP,FKBP1B,EPB41L4A-AS2,
MROH5,GPX8,GRM1,HTRA1,KCNS3,LOC344595,METTL7A,
MT1E,MT1L,NMU,NRK,PHLDB1,SGCE,TRIM58
ABHD14A,CALHM2,CSRP2,FADS1,FKBP9P1,GPX7,HRH2,
IKBIP,KCNS3,MAD2L2,MTA3,PDPN,PRY2,PTGIR,
SLC27A5,SLC43A3,SLFN12,SMOC2,TPRG1,TTC39C,XRRA1
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 KCNS3


There's no related Drug.
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Cross referenced IDs for KCNS3
* 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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