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 CERS6
Basic gene info.Gene symbolCERS6
Gene nameceramide synthase 6
SynonymsCERS5|LASS6
CytomapUCSC genome browser: 2q24.3
Genomic locationchr2 :169312758-169631644
Type of geneprotein-coding
RefGenesNM_001256126.1,
NM_203463.2,
Ensembl idENSG00000172292
DescriptionLAG1 homolog, ceramide synthase 6longevity assurance homolog 6
Modification date20141207
dbXrefs MIM : 615336
HGNC : HGNC
Ensembl : ENSG00000172292
HPRD : 17258
Vega : OTTHUMG00000132183
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CERS6
BioGPS: 253782
Gene Expression Atlas: ENSG00000172292
The Human Protein Atlas: ENSG00000172292
PathwayNCI Pathway Interaction Database: CERS6
KEGG: CERS6
REACTOME: CERS6
ConsensusPathDB
Pathway Commons: CERS6
MetabolismMetaCyc: CERS6
HUMANCyc: CERS6
RegulationEnsembl's Regulation: ENSG00000172292
miRBase: chr2 :169,312,758-169,631,644
TargetScan: NM_001256126
cisRED: ENSG00000172292
ContextiHOP: CERS6
cancer metabolism search in PubMed: CERS6
UCL Cancer Institute: CERS6
Assigned class in ccmGDBC

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Phenotypic Information for CERS6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CERS6
Familial Cancer Database: CERS6
* 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_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CERS6
MedGen: CERS6 (Human Medical Genetics with Condition)
ClinVar: CERS6
PhenotypeMGI: CERS6 (International Mouse Phenotyping Consortium)
PhenomicDB: CERS6

Mutations for CERS6
* 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
ovaryCERS6chr2169524445169524465CERS6chr2169524531169524551
pancreasCERS6chr2169578053169578073CERS6chr2169578116169578136
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 CERS6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE815041CERS6291312169630062169630167SPP113126648890433388904468
AW601963CERS652992169629012169629307TXNIP3005801145440113145440522
AW601881TXNIP114821145440113145440935CERS64836242169629012169629156
M86087LRFN5175144236101142361085CERS6762052169587955169588084
BF209028MEST5015717130146084130146155CERS65635822169374239169374258
BI050759CERS6252092169326774169326958SVIL191419102983953529839764
BE085594CERS6121072169406305169406402QSER1100166113292655232926618

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 # sample2  1    1      1 
GAIN (# sample)2  1    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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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=0

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=0)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no ns-snv.There's no s-snv.
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

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 41 1 21 51   7216
# mutation11 51 1 21 61   8216
nonsynonymous SNV11 51 1 21 41   2214
synonymous SNV           2    6  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
chr2:169417810p.A2T,CERS61
chr2:169571552p.L174F,CERS61
chr2:169312962p.V330A,CERS61
chr2:169622245p.L5L,CERS61
chr2:169417815p.D199Y,CERS61
chr2:169571583p.G333D,CERS61
chr2:169312971p.F8L,CERS61
chr2:169622254p.I200I,CERS61
chr2:169487532p.P340S1
chr2:169571584p.V19A,CERS61

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 CERS6 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 CERS6

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

AFF4,ARID2,CCNT1,DMXL1,DNAJB14,KIAA0232,LARP4,
CERS6,LCOR,LMBRD2,LRBA,RAPGEF6,RSC1A1,SPOPL,
STAM2,UBR1,UBR3,UEVLD,UHMK1,VEZF1,WDFY3
ANKRD50,ARID2,ATP7A,AVL9,SMIM14,DCAF10,ERO1LB,
FAM73A,FRS2,KIAA1958,CERS6,MAP9,PANK3,PEX1,
RALGAPB,SGPL1,SLC35A3,ZMYM2,ZNF281,ZNF587,ZNF678

ASXL2,ATF2,C9orf129,DDI2,DENND4C,GMCL1,INADL,
KIAA1715,CERS6,LATS1,PUM1,RAPGEF6,RC3H2,RIF1,
SERINC5,STRN,STT3B,TGFBRAP1,UBR3,UGGT1,UHMK1
ABLIM1,ARHGAP32,ATP7B,CASK,CMTM4,DOPEY2,GOLIM4,
IGF2BP2,KIAA0319L,KIAA1804,CERS6,MYO10,NEO1,PDXDC1,
PTPRK,RNF43,SH3RF2,SLC39A11,SSTR1,THSD4,XYLB
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 CERS6


There's no related Drug.
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Cross referenced IDs for CERS6
* 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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