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 KERA
Basic gene info.Gene symbolKERA
Gene namekeratocan
SynonymsCNA2|KTN|SLRR2B
CytomapUCSC genome browser: 12q22
Genomic locationchr12 :91444270-91452131
Type of geneprotein-coding
RefGenesNM_007035.3,
Ensembl idENSG00000139330
Descriptionkeratan sulfate proteoglycan keratocan
Modification date20141207
dbXrefs MIM : 603288
HGNC : HGNC
Ensembl : ENSG00000139330
HPRD : 04477
Vega : OTTHUMG00000170073
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KERA
BioGPS: 11081
Gene Expression Atlas: ENSG00000139330
The Human Protein Atlas: ENSG00000139330
PathwayNCI Pathway Interaction Database: KERA
KEGG: KERA
REACTOME: KERA
ConsensusPathDB
Pathway Commons: KERA
MetabolismMetaCyc: KERA
HUMANCyc: KERA
RegulationEnsembl's Regulation: ENSG00000139330
miRBase: chr12 :91,444,270-91,452,131
TargetScan: NM_007035
cisRED: ENSG00000139330
ContextiHOP: KERA
cancer metabolism search in PubMed: KERA
UCL Cancer Institute: KERA
Assigned class in ccmGDBC

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Phenotypic Information for KERA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: KERA
Familial Cancer Database: KERA
* 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_METABOLISM_OF_CARBOHYDRATES

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

Mutations for KERA
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows KERA 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 # sample              1  
GAIN (# sample)              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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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=52)
Stat. for Synonymous SNVs
(# total SNVs=18)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr12:91449939-91449939p.F40F4
chr12:91449250-91449250p.S270L3
chr12:91449844-91449844p.R72I3
chr12:91449902-91449902p.P53S2
chr12:91449722-91449722p.E113K2
chr12:91449223-91449223p.R279Q2
chr12:91449552-91449552p.T169T2
chr12:91449860-91449860p.P67S2
chr12:91449308-91449308p.D251Y2
chr12:91449866-91449866p.E65K2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample23 10  4  1 611  143 7
# mutation23 12  4  1 511  163 10
nonsynonymous SNV21 9  4  1 4 1  141 8
synonymous SNV 2 3       21   22 2
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
chr12:91449250p.S270L3
chr12:91449844p.L102V2
chr12:91449875p.R72I2
chr12:91449755p.G62C2
chr12:91449939p.R142K2
chr12:91449634p.F40F2
chr12:91449298p.L309L1
chr12:91449493p.N206I1
chr12:91450050p.E113K1
chr12:91445220p.T36T1

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 KERA 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 KERA

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

AMELX,C17orf51,CAPZA2,COL25A1,FAT3,FSTL5,GAS2,
IGLON5,KERA,MEOX2,MET,NPTX2,SCX,ST7-OT3,
ST7-OT4,TG,THBS4,TMEFF2,AGMO,TNMD,WIF1
ADH4,CBLN4,CHP2,DCC,AMER2,GPR151,GRIN3A,
GUCA2B,HAPLN1,HTR3D,KCNH5,KERA,LIN28B,LINC00461,
NCAN,ONECUT2,OR4E2,PRSS33,RAI14,TCAM1P,TGM6

ADCY2,C1S,CPZ,DCN,DOK5,DZIP1,MICU3,
GUCY1A3,KERA,LOC399959,LUM,MITF,NCAM2,NKX3-2,
PABPC5,PDE1A,PPP1R3C,PRDM6,RNF180,SDC2,SSPN
ACTA1,BTG4,TEX36,SMIM21,CCKAR,CRISPLD1,CRYGD,
PIH1D3,DAPL1,FMO2,GOLGA8F,GRPR,HMGCLL1,KERA,
KRTAP13-4,LCE1B,LPPR5,LUZP4,OR2L3,PPAPDC1A,RPRM
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 KERA


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