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 SEC31A

Basic gene info.	Gene symbol	SEC31A
	Gene name	SEC31 homolog A (S. cerevisiae)
	Synonyms	ABP125\|ABP130\|HSPC334\|SEC31L1
	Cytomap	UCSC genome browser: 4q21.22
	Genomic location	chr4 :83739813-83812412
	Type of gene	protein-coding
	RefGenes	NM_001077206.2, NM_001077207.2,NM_001077208.2,NM_001191049.1,NM_001300744.1, NM_001300745.1,NM_014933.3,NM_016211.3,
	Ensembl id	ENSG00000138674
	Description	SEC31-like protein 1SEC31-related protein Aprotein transport protein Sec31Aweb1-like proteinyeast Sec31p homolog
	Modification date	20141222
dbXrefs	MIM : 610257
	HGNC : HGNC
	Ensembl : ENSG00000138674
	HPRD : 15314
	Vega : OTTHUMG00000130297
Protein	UniProt: O94979 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SEC31A
	BioGPS: 22872
	Gene Expression Atlas: ENSG00000138674
	The Human Protein Atlas: ENSG00000138674
Pathway	NCI Pathway Interaction Database: SEC31A
	KEGG: SEC31A
	REACTOME: SEC31A
	ConsensusPathDB
	Pathway Commons: SEC31A
Metabolism	MetaCyc: SEC31A
	HUMANCyc: SEC31A
Regulation	Ensembl's Regulation: ENSG00000138674
	miRBase: chr4 :83,739,813-83,812,412
	TargetScan: NM_001077206
	cisRED: ENSG00000138674
Context	iHOP: SEC31A
	cancer metabolism search in PubMed: SEC31A
	UCL Cancer Institute: SEC31A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for SEC31A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SEC31A
	Familial Cancer Database: SEC31A

* 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	610257; gene. 610257; gene.
Orphanet
Disease	KEGG Disease: SEC31A
	MedGen: SEC31A (Human Medical Genetics with Condition)
	ClinVar: SEC31A
Phenotype	MGI: SEC31A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SEC31A

Mutations for SEC31A

* 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

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
breast	SEC31A	chr4	83745022	83745022		chr8	98250842	98250842
breast	SEC31A	chr4	83745137	83745137	PTDSS1	chr8	97336521	97336521
ovary	SEC31A	chr4	83749481	83749501	SCD5	chr4	83677766	83677786

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 SEC31A 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
BI052970	SEC31A	1	317	4	83765556	83770072	LRCH4	317	374	7	100174335	100174392
DT220653	SMC1A	1	218	X	53449439	53449656	SEC31A	216	397	4	83748664	83750212
BM992139	SEC31A	8	426	4	83740164	83745811	ARPC5	422	672	1	183602237	183604849
BI823499	SEC31A	1	459	4	83799881	83812291	PTEN	456	804	10	89725042	89725387
CA419101	MTA3	263	306	2	42731318	42731361	SEC31A	305	694	4	83768137	83768533
BF751621	SEC31A	44	427	4	83819174	83821677	MEMO1	412	486	2	32094983	32108490
AV746752	SEC31A	1	61	4	83741210	83741270	SEC31A	58	393	4	83742092	83742435
AI523884	SEC31A	3	205	4	83814162	83814364	FUBP1	200	543	1	78443241	78443584
BF839137	CTPS2	172	304	X	16672561	16672693	SEC31A	298	505	4	83803618	83803824
DT219678	SMC1A	1	218	X	53449439	53449656	SEC31A	216	659	4	83745708	83750212
BF824998	CD101	24	370	1	117576519	117576864	SEC31A	366	491	4	83740102	83740227
BP418474	SEC31A	14	103	4	83741591	83741680	ARFGAP1	103	439	20	61919448	61919784
DB231724	PHF15	1	94	5	133860086	133860179	SEC31A	94	555	4	83799883	83812295
AF161393	SEC31A	1	1562	4	83739814	83765613	BCKDHB	1559	1578	6	80865557	80865576
CR933696	SEC31A	1	3687	4	83739814	83812306	BCKDHB	3684	3703	6	80865557	80865576
AL049463	SEC31A	1	571	4	83739814	83740384	PPP2R2C	562	587	4	6410602	6410627
AF161452	SEC31A	1	1382	4	83739814	83763567	BCKDHB	1379	1398	6	80865557	80865576

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

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)

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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=1

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=1)	Stat. for Synonymous SNVs (# total SNVs=0)
	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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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
chr4:83778206-83778206	p.R555C	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	3	4		12	1		6		5			11	6	3		1	7	10		14
# mutation	3	4		12	1		6		5			12	6	3		1	7	10		18
nonsynonymous SNV	1	4		7	1		5		1			10	6	2			4	6		12
synonymous SNV	2			5			1		4			2		1		1	3	4		6

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
chr4:83763465	p.R744C,SEC31A	2
chr4:83770112	p.A893A,SEC31A	2
chr4:83802025	p.S324G,SEC31A	1
chr4:83784523	p.A111T,SEC31A	1
chr4:83770070	p.F975F,SEC31A	1
chr4:83791497	p.P771P,SEC31A	1
chr4:83748729	p.C550S,SEC31A	1
chr4:83778105	p.D320D,SEC31A	1
chr4:83796937	p.I102L,SEC31A	1
chr4:83802064	p.P960L,SEC31A	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 SEC31A 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 SEC31A

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


ADAMTS12,ANXA5,ARCN1,ENTPD7,FAM114A1,FBN1,ITGAV, LIN54,PRRC1,SEC23A,SEC24A,SEC24B,SEC24D,SEC31A, SLAIN2,SLC10A7,TBC1D8B,TCF12,TJP1,USO1,VCAN	AGFG1,AGPS,AHCYL1,AP3M1,ARCN1,ARHGAP21,CALU, CDC27,CLTC,EXOC5,GNG12,HGSNAT,LUZP6,RABL3, SEC22B,SEC31A,SLC35B4,TMEM167A,VAMP7,CHMP3,XPOT

ANTXR1,ARHGAP1,BMPR2,EHD2,FBXL7,FIBIN,FKBP7, FSTL1,FZD1,ITGAV,LAMA4,LAMC1,LTBP1,SEC31A, SGCD,SNX18,SPOCK1,SSPN,TCF4,TIMP2,TSHZ3	AHCYL1,ALS2,ARID1B,BAZ2B,CEP120,CREB3L2,FAM168A, FBXW2,GIGYF2,GIT2,GTF2IP1,MAPKBP1,NBAS,NFATC3, PCM1,PCNX,SEC31A,SMC3,UBR1,ZNF106,ZNF507

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 SEC31A

There's no related Drug.

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Cross referenced IDs for SEC31A

* 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