Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	CERS6
	Gene name	ceramide synthase 6
	Synonyms	CERS5\|LASS6
	Cytomap	UCSC genome browser: 2q24.3
	Genomic location	chr2 :169312758-169631644
	Type of gene	protein-coding
	RefGenes	NM_001256126.1, NM_203463.2,
	Ensembl id	ENSG00000172292
	Description	LAG1 homolog, ceramide synthase 6longevity assurance homolog 6
	Modification date	20141207
dbXrefs	MIM : 615336
	HGNC : HGNC
	Ensembl : ENSG00000172292
	HPRD : 17258
	Vega : OTTHUMG00000132183
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CERS6
	BioGPS: 253782
	Gene Expression Atlas: ENSG00000172292
	The Human Protein Atlas: ENSG00000172292
Pathway	NCI Pathway Interaction Database: CERS6
	KEGG: CERS6
	REACTOME: CERS6
	ConsensusPathDB
	Pathway Commons: CERS6
Metabolism	MetaCyc: CERS6
	HUMANCyc: CERS6
Regulation	Ensembl's Regulation: ENSG00000172292
	miRBase: chr2 :169,312,758-169,631,644
	TargetScan: NM_001256126
	cisRED: ENSG00000172292
Context	iHOP: CERS6
	cancer metabolism search in PubMed: CERS6
	UCL Cancer Institute: CERS6
Assigned class in ccmGDB	C

Top

Phenotypic Information for CERS6(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: CERS6
	MedGen: CERS6 (Human Medical Genetics with Condition)
	ClinVar: CERS6
Phenotype	MGI: CERS6 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

Top

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	CERS6	chr2	169524445	169524465	CERS6	chr2	169524531	169524551
pancreas	CERS6	chr2	169578053	169578073	CERS6	chr2	169578116	169578136

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CERS6 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
BE815041	CERS6	29	131	2	169630062	169630167	SPP1	131	266	4	88904333	88904468
AW601963	CERS6	5	299	2	169629012	169629307	TXNIP	300	580	1	145440113	145440522
AW601881	TXNIP	11	482	1	145440113	145440935	CERS6	483	624	2	169629012	169629156
M86087	LRFN5	1	75	14	42361011	42361085	CERS6	76	205	2	169587955	169588084
BF209028	MEST	501	571	7	130146084	130146155	CERS6	563	582	2	169374239	169374258
BI050759	CERS6	25	209	2	169326774	169326958	SVIL	191	419	10	29839535	29839764
BE085594	CERS6	12	107	2	169406305	169406402	QSER1	100	166	11	32926552	32926618

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

Top

SNV 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

Top

Somatic 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.

Top

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

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		4	1		1		2	1		5	1				7	2	1	6
# mutation	1	1		5	1		1		2	1		6	1				8	2	1	6
nonsynonymous SNV	1	1		5	1		1		2	1		4	1				2	2	1	4
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])

Top

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
chr2:169571586	p.F32F,CERS6	1
chr2:169313014	p.V214A,CERS6	1
chr2:169626093	p.A362A,CERS6	1
chr2:169547564	p.P33Q,CERS6	1
chr2:169571606	p.F217L,CERS6	1
chr2:169313054	p.A35V,CERS6	1
chr2:169626103	p.A228T,CERS6	1
chr2:169547576	p.D37Y,CERS6	1
chr2:169571631	p.A228V,CERS6	1
chr2:169313056	p.P62P,CERS6	1

Other 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

Copy 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]

Top

Gene Expression for CERS6

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for CERS6

There's no related Drug.

Top

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