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

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 SEC13

Basic gene info.	Gene symbol	SEC13
	Gene name	SEC13 homolog (S. cerevisiae)
	Synonyms	D3S1231E\|SEC13L1\|SEC13R\|npp-20
	Cytomap	UCSC genome browser: 3p25-p24
	Genomic location	chr3 :10342614-10362725
	Type of gene	protein-coding
	RefGenes	NM_001136026.2, NM_001136232.2,NM_001278946.1,NM_030673.3,NM_183352.2,
	Ensembl id	ENSG00000157020
	Description	SEC13-like 1 isoformSEC13-like protein 1SEC13-related proteinprotein SEC13 homolog
	Modification date	20141207
dbXrefs	MIM : 600152
	HGNC : HGNC
	Ensembl : ENSG00000157020
	HPRD : 02538
	Vega : OTTHUMG00000128671
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SEC13
	BioGPS: 6396
	Gene Expression Atlas: ENSG00000157020
	The Human Protein Atlas: ENSG00000157020
Pathway	NCI Pathway Interaction Database: SEC13
	KEGG: SEC13
	REACTOME: SEC13
	ConsensusPathDB
	Pathway Commons: SEC13
Metabolism	MetaCyc: SEC13
	HUMANCyc: SEC13
Regulation	Ensembl's Regulation: ENSG00000157020
	miRBase: chr3 :10,342,614-10,362,725
	TargetScan: NM_001136026
	cisRED: ENSG00000157020
Context	iHOP: SEC13
	cancer metabolism search in PubMed: SEC13
	UCL Cancer Institute: SEC13
Assigned class in ccmGDB	C

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Phenotypic Information for SEC13(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SEC13
	Familial Cancer Database: SEC13

* 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_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: SEC13
	MedGen: SEC13 (Human Medical Genetics with Condition)
	ClinVar: SEC13
Phenotype	MGI: SEC13 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SEC13

Mutations for SEC13

* 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

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SEC13 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
BG256737	MRPS10	1	339	6	42175255	42175596	SEC13	335	725	3	10343270	10343668
DW441224	TOMM7	18	262	7	22857627	22862498	SEC13	257	379	3	10342765	10342887
BE161424	KHNYN	24	77	14	24908767	24908820	SEC13	72	549	3	10343009	10353671

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=25)	Stat. for Synonymous SNVs (# total SNVs=8)

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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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
chr3:10354352-10354352	p.S76L	2
chr3:10346764-10346764	p.A221T	2
chr3:10357052-10357052	p.I39I	2
chr3:10354321-10354321	p.W86*	2
chr3:10357109-10357109	p.Q20H	2
chr3:10346828-10346828	p.D199D	2
chr3:10342967-10342967	p.E316G	1
chr3:10354338-10354338	p.R81W	1
chr3:10345799-10345799	p.K256*	1
chr3:10347261-10347261	p.N189S	1

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

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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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
chr3:10346828	p.D185D,SEC13	2
chr3:10357052	p.I25I,SEC13	2
chr3:10342967	p.E302A,SEC13	1
chr3:10346776	p.G124G,SEC13	1
chr3:10354321	p.E302Q,SEC13	1
chr3:10342968	p.P99P,SEC13	1
chr3:10346789	p.S295S,SEC13	1
chr3:10354336	p.C96C,SEC13	1
chr3:10342987	p.G281R,SEC13	1
chr3:10346791	p.D89N,SEC13	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 SEC13 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 SEC13

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))

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CNV 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

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


ARPC4,KXD1,PRADC1,BRK1,CIDECP,COPE,CTU2, DDX49,FAM58A,IL17RC,JAGN1,MED8,MOGS,MTMR14, OGG1,POLR2F,PRDX4,RPUSD3,SEC13,TADA3,TATDN2	ADRM1,AP2S1,ARHGDIA,ASNA1,KXD1,CHMP2A,COPE, CUEDC2,DRAP1,GNB2,MRPL28,NAA10,PSMC3,PSMC4, LAMTOR2,SDF4,SEC13,SLC39A3,USP5,YIF1A,YKT6

AGR2,ARF4,ARPC4,GSKIP,C19orf10,CYSTM1,CIB1, COPE,CYB561D2,JAGN1,MPDU1,MRPL54,NDUFC1,POLR2L, PPIB,RPN1,S100P,SEC13,SEC61B,SERF2,SRA1	AKR1A1,ATOX1,COA4,CNPY2,COQ6,GLRX,GLYATL1, GOSR2,GSTO1,NTMT1,MRPL55,P4HB,PPAPDC1B,SEC13, SEC24D,SLC35B1,SNRPA1,TFEC,TSPO2,YIF1A,YIPF5

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

: Open all plots for all cancer types

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Interacting 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 SEC13

There's no related Drug.

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Cross referenced IDs for SEC13

* 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