Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 SSR2
Basic gene info.Gene symbolSSR2
Gene namesignal sequence receptor, beta (translocon-associated protein beta)
SynonymsTLAP|TRAP-BETA|TRAPB
CytomapUCSC genome browser: 1q21-q23
Genomic locationchr1 :155978838-155990758
Type of geneprotein-coding
RefGenesNM_003145.3,
Ensembl idENSG00000163479
DescriptionSSR-betasignal sequence receptor subunit betatranslocon-associated protein betatranslocon-associated protein subunit beta
Modification date20141207
dbXrefs MIM : 600867
HGNC : HGNC
Ensembl : ENSG00000163479
HPRD : 02923
Vega : OTTHUMG00000017456
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SSR2
BioGPS: 6746
Gene Expression Atlas: ENSG00000163479
The Human Protein Atlas: ENSG00000163479
PathwayNCI Pathway Interaction Database: SSR2
KEGG: SSR2
REACTOME: SSR2
ConsensusPathDB
Pathway Commons: SSR2
MetabolismMetaCyc: SSR2
HUMANCyc: SSR2
RegulationEnsembl's Regulation: ENSG00000163479
miRBase: chr1 :155,978,838-155,990,758
TargetScan: NM_003145
cisRED: ENSG00000163479
ContextiHOP: SSR2
cancer metabolism search in PubMed: SSR2
UCL Cancer Institute: SSR2
Assigned class in ccmGDBC

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Phenotypic Information for SSR2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SSR2
Familial Cancer Database: SSR2
* 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SSR2
MedGen: SSR2 (Human Medical Genetics with Condition)
ClinVar: SSR2
PhenotypeMGI: SSR2 (International Mouse Phenotyping Consortium)
PhenomicDB: SSR2

Mutations for SSR2
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SSR2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CA335796SSR212301155979019155979248ZNF738225608192156163221562015
AA576517SSR211551155978843155978997AAK115143726974609269746377
AA372679SSR21581155979239155979296SSR2563031155978969155979215
BF326256IGF2BP3320572343631223436512SSR21955971155979325155988158
BE837584FUCA211966143816937143823381SSR21816351155979271155988155
BM811163PAPD723120567530256753123SSR21188501155979190155990704

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample   1    1 1      
GAIN (# sample)   1    1 1      
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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check002.gifSNV 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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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=12)
Stat. for Synonymous SNVs
(# total SNVs=9)
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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr1:155989853-155989853p.E36*2
chr1:155989860-155989860p.Y33Y2
chr1:155981618-155981618p.R142*2
chr1:155984806-155984806p.F103L1
chr1:155989841-155989841p.L40L1
chr1:155979398-155979398p.G162D1
chr1:155984845-155984845p.S90S1
chr1:155979424-155979424p.F153F1
chr1:155984846-155984846p.S90F1
chr1:155981610-155981610p.S144S1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample1112  2 1  13   3  1
# mutation1112  2 1  13   3  1
nonsynonymous SNV 1 2  1    12   1   
synonymous SNV1 1   1 1   1   2  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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr1:155989841p.V57V1
chr1:155981632p.A54A1
chr1:155989874p.Q43Q1
chr1:155981652p.L40L1
chr1:155989878p.L29L1
chr1:155984754p.K27N1
chr1:155989899p.G20G1
chr1:155984777p.G162D1
chr1:155984778p.F153F1
chr1:155984846p.R137L1

check002.gifOther 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

check002.gifCopy Number for SSR2 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 SSR2

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

APOA1BP,C1orf85,CCT3,DPM3,EFNA4,HAX1,JTB,
KRTCAP2,MRPL24,MRPL9,MRPS21,PMF1,PRCC,PSMB4,
PSMD4,RAB25,LAMTOR2,SCNM1,SSR2,UFC1,VPS72
BTF3,COPZ1,CUTA,DGUOK,ERGIC3,GNB2L1,LSM2,
PPIA,PPIH,RPL10A,RPL24,RPL27A,RPL35A,RPL41,
RPS11,RPS24,RPS4X,RPS7,RPSAP58,SNRPF,SSR2

ARF1,C19orf10,C1orf43,HAX1,ILF2,JTB,MRPL24,
MTX1,OSTC,PMF1,PSMB4,PSMD4,RBM34,LAMTOR2,
SNAPIN,SRP9,SSR2,TIPRL,TMEM183A,UFC1,VPS72
ALG5,C12orf57,TIMMDC1,COPZ1,DPY30,EEF1B2,MCEE,
NAA20,OSTC,RPL24,RPL27A,RPL35,RPL35A,RPL41,
RPS3A,RPS6,RPSAP58,SERF2,SNRPD2,SSR2,UFC1
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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 SSR2


There's no related Drug.
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Cross referenced IDs for SSR2
* 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



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