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 SSR1
Basic gene info.Gene symbolSSR1
Gene namesignal sequence receptor, alpha
SynonymsTRAPA
CytomapUCSC genome browser: 6p24.3
Genomic locationchr6 :7281287-7313541
Type of geneprotein-coding
RefGenesNM_001292008.1,
NM_003144.4,NR_120448.1,
Ensembl idENSG00000124783
DescriptionSSR alpha subunitSSR-alphaTRAP alphaTRAP-alphasignal sequence receptor subunit alphatranslocon-associated protein alpha subunittranslocon-associated protein subunit alpha
Modification date20141207
dbXrefs MIM : 600868
HGNC : HGNC
Ensembl : ENSG00000124783
HPRD : 02924
Vega : OTTHUMG00000014202
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SSR1
BioGPS: 6745
Gene Expression Atlas: ENSG00000124783
The Human Protein Atlas: ENSG00000124783
PathwayNCI Pathway Interaction Database: SSR1
KEGG: SSR1
REACTOME: SSR1
ConsensusPathDB
Pathway Commons: SSR1
MetabolismMetaCyc: SSR1
HUMANCyc: SSR1
RegulationEnsembl's Regulation: ENSG00000124783
miRBase: chr6 :7,281,287-7,313,541
TargetScan: NM_001292008
cisRED: ENSG00000124783
ContextiHOP: SSR1
cancer metabolism search in PubMed: SSR1
UCL Cancer Institute: SSR1
Assigned class in ccmGDBC

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Phenotypic Information for SSR1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SSR1
MedGen: SSR1 (Human Medical Genetics with Condition)
ClinVar: SSR1
PhenotypeMGI: SSR1 (International Mouse Phenotyping Consortium)
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.

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 SSR1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF818212SSR11203672845357284737AVL920025173304236933042420
M14219DCN261292129153970491576454SSR112921778672880537288539
BQ353656C5AR11184194782396847824151SSR1176282672887717288877
AI082662SSR133185673007607300912RBFOX2182402223642312436423345
BP386202SSR11313672816047281915PSMA1314500111452642414526610
AW392218SSR122144672885347288657SRPK21356367104783707104808498
BF756608SSR11162672956947299038NOTCH21572451120456798120456886
BE936569SSR187308672988537299072HPS32994533148885009148889926
BM728644SSR11116672838727283987SSR1109677672851127285680
AK025753SSR11367672840717284437SSR13632291672849497286878

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 # sample3     1      2  1
GAIN (# sample)3            2  1
LOSS (# sample)      1          
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=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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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
chr6:7310259-7310259p.L28S2
chr6:7299032-7299032p.F190V2
chr6:7290115-7290115p.S281S1
chr6:7301565-7301565p.N174S1
chr6:7310175-7310175p.V56E1
chr6:7290155-7290155p.S268L1
chr6:7301590-7301590p.G166R1
chr6:7310176-7310176p.V56L1
chr6:7290170-7290170p.?1
chr6:7301605-7301605p.A161P1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1114  1    1    3  2
# mutation1114  1    1    3  3
nonsynonymous SNV11 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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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
chr6:7290155p.G98R,SSR11
chr6:7303849p.A161P1
chr6:7295626p.L140P1
chr6:7310176p.D129E1
chr6:7295711p.F124F1
chr6:7310258p.A122A1
chr6:7299013p.I87V,SSR11
chr6:7313292p.D72N,SSR11
chr6:7301590p.V56L,SSR11
chr6:7301605p.L28L,SSR11

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 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

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

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
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 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



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