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 SSR1

Basic gene info.	Gene symbol	SSR1
	Gene name	signal sequence receptor, alpha
	Synonyms	TRAPA
	Cytomap	UCSC genome browser: 6p24.3
	Genomic location	chr6 :7281287-7313541
	Type of gene	protein-coding
	RefGenes	NM_001292008.1, NM_003144.4,NR_120448.1,
	Ensembl id	ENSG00000124783
	Description	SSR alpha subunitSSR-alphaTRAP alphaTRAP-alphasignal sequence receptor subunit alphatranslocon-associated protein alpha subunittranslocon-associated protein subunit alpha
	Modification date	20141207
dbXrefs	MIM : 600868
	HGNC : HGNC
	Ensembl : ENSG00000124783
	HPRD : 02924
	Vega : OTTHUMG00000014202
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SSR1
	BioGPS: 6745
	Gene Expression Atlas: ENSG00000124783
	The Human Protein Atlas: ENSG00000124783
Pathway	NCI Pathway Interaction Database: SSR1
	KEGG: SSR1
	REACTOME: SSR1
	ConsensusPathDB
	Pathway Commons: SSR1
Metabolism	MetaCyc: SSR1
	HUMANCyc: SSR1
Regulation	Ensembl's Regulation: ENSG00000124783
	miRBase: chr6 :7,281,287-7,313,541
	TargetScan: NM_001292008
	cisRED: ENSG00000124783
Context	iHOP: SSR1
	cancer metabolism search in PubMed: SSR1
	UCL Cancer Institute: SSR1
Assigned class in ccmGDB	C

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Phenotypic Information for SSR1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SSR1
	Familial Cancer Database: SSR1

* 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: SSR1
	MedGen: SSR1 (Human Medical Genetics with Condition)
	ClinVar: SSR1
Phenotype	MGI: SSR1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SSR1

Mutations for SSR1

* 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 SSR1 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
BF818212	SSR1	1	203	6	7284535	7284737	AVL9	200	251	7	33042369	33042420
M14219	DCN	26	1292	12	91539704	91576454	SSR1	1292	1778	6	7288053	7288539
BQ353656	C5AR1	1	184	19	47823968	47824151	SSR1	176	282	6	7288771	7288877
AI082662	SSR1	33	185	6	7300760	7300912	RBFOX2	182	402	22	36423124	36423345
BP386202	SSR1	1	313	6	7281604	7281915	PSMA1	314	500	11	14526424	14526610
AW392218	SSR1	22	144	6	7288534	7288657	SRPK2	135	636	7	104783707	104808498
BF756608	SSR1	1	162	6	7295694	7299038	NOTCH2	157	245	1	120456798	120456886
BE936569	SSR1	87	308	6	7298853	7299072	HPS3	299	453	3	148885009	148889926
BM728644	SSR1	1	116	6	7283872	7283987	SSR1	109	677	6	7285112	7285680
AK025753	SSR1	1	367	6	7284071	7284437	SSR1	363	2291	6	7284949	7286878

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=20)	Stat. for Synonymous SNVs (# total SNVs=1)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr6:7299032-7299032	p.F190V	2
chr6:7310259-7310259	p.L28S	2
chr6:7295711-7295711	p.R236K	1
chr6:7301720-7301720	p.A122A	1
chr6:7313280-7313280	p.P25H	1
chr6:7298980-7298980	p.T207I	1
chr6:7301730-7301730	p.S119F	1
chr6:7313292-7313292	p.F21S	1
chr6:7299004-7299004	p.R199T	1
chr6:7303804-7303804	p.I87V	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=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	1	4			1					1					3			2
# mutation	1	1	1	4			1					1					3			3
nonsynonymous SNV	1	1		4			1					1								3
synonymous SNV			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
chr6:7301667	p.I87V,SSR1	1
chr6:7301699	p.D72N,SSR1	1
chr6:7301714	p.V56L,SSR1	1
chr6:7301720	p.L28L,SSR1	1
chr6:7303804	p.F21S,SSR1	1
chr6:7290155	p.S200L,SSR1	1
chr6:7303849	p.I196I,SSR1	1
chr6:7295626	p.R168K,SSR1	1
chr6:7310176	p.V128G,SSR1	1
chr6:7295711	p.G98R,SSR1	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 SSR1 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 SSR1

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


ACTR2,CDYL,DDX18,KDM1B,KPNA4,LOC221710,MRPL19, MRS2,BLOC1S5,NUP153,PAK1IP1,PRPF4B,RIOK1,RNGTT, SLC35B3,SRP72,SRPK1,SSR1,STT3A,SYNCRIP,TXNDC5	BET1,HIAT1,HSPA13,NRAS,NUS1,NXT2,RAB14, SLC30A5,SPCS3,SPTLC1,SSR1,TM9SF3,TMED10,TMED2, TMED7,TMX1,TRAM1,TWF1,UBLCP1,UFM1,YIPF5

AGR2,C19orf10,SLC18B1,EEF1E1,GMDS,HSPA5,IBTK, LRRC16A,NOL7,NUCB2,NUS1,OSTC,PGM3,SLC39A7, SNRNP48,SPCS3,SSR1,SSR3,STT3A,TMED2,TXNDC5	CALR,CANX,CAPRIN1,CRELD2,DNAJB11,DNAJC3,ENO1, HIF1A,HSP90B1,HSPA5,HYOU1,LRRC59,PDIA3,PDIA3P1, PDIA4,PSMD12,RNF145,RPN2,SEC61A1,SSR1,STT3A

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 SSR1

There's no related Drug.

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Cross referenced IDs for SSR1

* 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