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 SSR3

Basic gene info.	Gene symbol	SSR3
	Gene name	signal sequence receptor, gamma (translocon-associated protein gamma)
	Synonyms	TRAPG
	Cytomap	UCSC genome browser: 3q25.31
	Genomic location	chr3 :156257928-156272973
	Type of gene	protein-coding
	RefGenes	NM_007107.3,
	Ensembl id	ENSG00000114850
	Description	SSR gammaSSR-gammaTRAP-complex gamma subunitTRAP-gammasignal sequence receptor subunit gammatranslocon-associated protein gamma subunittranslocon-associated protein subunit gamma
	Modification date	20141207
dbXrefs	MIM : 606213
	HGNC : HGNC
	Ensembl : ENSG00000114850
	HPRD : 16206
	Vega : OTTHUMG00000158632
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SSR3
	BioGPS: 6747
	Gene Expression Atlas: ENSG00000114850
	The Human Protein Atlas: ENSG00000114850
Pathway	NCI Pathway Interaction Database: SSR3
	KEGG: SSR3
	REACTOME: SSR3
	ConsensusPathDB
	Pathway Commons: SSR3
Metabolism	MetaCyc: SSR3
	HUMANCyc: SSR3
Regulation	Ensembl's Regulation: ENSG00000114850
	miRBase: chr3 :156,257,928-156,272,973
	TargetScan: NM_007107
	cisRED: ENSG00000114850
Context	iHOP: SSR3
	cancer metabolism search in PubMed: SSR3
	UCL Cancer Institute: SSR3
Assigned class in ccmGDB	C

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Phenotypic Information for SSR3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SSR3
	Familial Cancer Database: SSR3

* 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: SSR3
	MedGen: SSR3 (Human Medical Genetics with Condition)
	ClinVar: SSR3
Phenotype	MGI: SSR3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SSR3

Mutations for SSR3

* 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 SSR3 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
BP379122	SSR3	2	408	3	156266669	156272897	UBA3	401	551	3	69126984	69129507
AW168600	SSR3	10	118	3	156257933	156258040	MACF1	104	296	1	39881325	39881517
AW838201	SSR3	1	159	3	156260819	156260977	SSR3	157	394	3	156259374	156259611
AI159851	SSR3	1	226	3	156257933	156258158	KIF3B	224	467	20	30920942	30921185
AI973221	SSR3	1	170	3	156259099	156259268	CPEB4	163	399	5	173384876	173385112
AW838512	SSR3	19	307	3	156260688	156260977	SSR3	305	404	3	156259374	156259473
BQ772087	SSR3	19	314	3	156259100	156259394	PRPF6	311	756	20	62613241	62613686
AI096496	SSR3	1	224	3	156257935	156258158	KIF3B	222	500	20	30920907	30921185
AW994363	SSR3	1	478	3	156261017	156272827	SATB1	475	665	3	18419661	18428351
AI380153	SSR3	1	222	3	156257937	156258158	KIF3B	220	429	20	30920976	30921185

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=14)	Stat. for Synonymous SNVs (# total SNVs=6)

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
chr3:156262178-156262178	p.S137C	2
chr3:156266737-156266737	p.E106K	2
chr3:156266774-156266774	p.E93E	2
chr3:156271452-156271452	p.L84L	2
chr3:156262158-156262158	p.L144L	2
chr3:156271470-156271470	p.K78N	2
chr3:156272757-156272757	p.A41V	1
chr3:156262185-156262185	p.T135A	1
chr3:156272846-156272846	p.S11S	1
chr3:156262232-156262232	p.?	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		1	1				1			1		2				1		1		4
# mutation		1	1				1			1		3				1		1		4
nonsynonymous SNV			1							1		2				1		1		4
synonymous SNV		1					1					1

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
chr3:156266708	p.K115K	2
chr3:156266745	p.L84L	1
chr3:156266748	p.Y77C	1
chr3:156271452	p.A41V	1
chr3:156271474	p.L31L	1
chr3:156272757	p.Q10R	1
chr3:156272786	p.S7F	1
chr3:156260995	p.K185K	1
chr3:156272850	p.I156V	1
chr3:156262122	p.R114W	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 SSR3 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 SSR3

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


COPB2,DCUN1D1,DHX36,EIF2A,FNDC3B,FYTTD1,GMPS, GYG1,KPNA4,NMD3,PDCD10,RNF13,RSRC1,SEC61A1, SERP1,SLC33A1,SRPRB,SSR1,SSR3,STT3A,TMED2	API5,ARL1,ATG5,COPB1,ERLEC1,GOLPH3,HIAT1, JKAMP,LOC653566,NUS1,PIGK,RAB14,SPTLC1,SSR1, SSR3,TM9SF3,TMED10,TMED2,TMED7,TRAM1,TWF1

ABHD10,ARF4,C19orf10,ERLEC1,FKBP11,GOLT1B,HSPA13, NMD3,OSTC,PGM3,RPN1,SELT,SERP1,SLC33A1, SPCS3,SRPRB,SSR1,SSR3,TMED2,TMED7,TMEM39A	ALG5,ANXA7,EMC7,C19orf10,CISD2,ERLEC1,HAUS1, NAA20,NUP37,OSTC,PRDX4,PREB,RAN,RPL26L1, SEC11C,SNRNP40,SRPRB,SSR3,TMED2,TMEM165,TOMM5

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 SSR3

There's no related Drug.

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Cross referenced IDs for SSR3

* 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