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 STT3A
Basic gene info.Gene symbolSTT3A
Gene nameSTT3A, subunit of the oligosaccharyltransferase complex (catalytic)
SynonymsITM1|STT3-A|TMC
CytomapUCSC genome browser: 11q23.3
Genomic locationchr11 :125462738-125491280
Type of geneprotein-coding
RefGenesNM_001278503.1,
NM_001278504.1,NM_152713.4,
Ensembl idENSG00000134910
DescriptionB5STT3, subunit of the oligosaccharyltransferase complex, homolog ASTT3A, cataylic subunit of the oligosaccharyltransferase complexdolichyl-diphosphooligosaccharide protein glycotransferasedolichyl-diphosphooligosaccharide--protein glycosyltransferase
Modification date20141219
dbXrefs MIM : 601134
HGNC : HGNC
Ensembl : ENSG00000134910
HPRD : 03086
Vega : OTTHUMG00000165852
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_STT3A
BioGPS: 3703
Gene Expression Atlas: ENSG00000134910
The Human Protein Atlas: ENSG00000134910
PathwayNCI Pathway Interaction Database: STT3A
KEGG: STT3A
REACTOME: STT3A
ConsensusPathDB
Pathway Commons: STT3A
MetabolismMetaCyc: STT3A
HUMANCyc: STT3A
RegulationEnsembl's Regulation: ENSG00000134910
miRBase: chr11 :125,462,738-125,491,280
TargetScan: NM_001278503
cisRED: ENSG00000134910
ContextiHOP: STT3A
cancer metabolism search in PubMed: STT3A
UCL Cancer Institute: STT3A
Assigned class in ccmGDBC

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Phenotypic Information for STT3A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: STT3A
Familial Cancer Database: STT3A
* 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: STT3A
MedGen: STT3A (Human Medical Genetics with Condition)
ClinVar: STT3A
PhenotypeMGI: STT3A (International Mouse Phenotyping Consortium)
PhenomicDB: STT3A

Mutations for STT3A
* 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 STT3A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
EC545946STT3A16611125488308125488374CKB5910314103986331103986376
AU139929STT3A128711125462749125472235LIPG280654184709171547095841
BE696961STT3A178811125462999125463073GJA1811876121769334121769440
CN404588STT3A127011125463926125464195LRRC47268609136969023697243
BE837748STT3A5219411125474050125475574UBQLN41834991156013163156013479
BF803158STT3A2229211125490436125490703PTPN2327343334745029247450452
AW366596CARKD27833813111290474111290534STT3A33946211125474095125475599
AW366584CARKD24530513111290474111290534STT3A30642911125474095125475599

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
There's no copy number variation information in COSMIC data for this gene.

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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=46)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr11:125488282-125488282p.L597I2
chr11:125481361-125481361p.R386W2
chr11:125483055-125483055p.R513C2
chr11:125482500-125482500p.L408P2
chr11:125474106-125474106p.I158V2
chr11:125488267-125488267p.?2
chr11:125481352-125481352p.S383P1
chr11:125474113-125474113p.R160Q1
chr11:125476316-125476316p.L246M1
chr11:125483013-125483013p.R499G1

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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
# sample1 14  1 3  84  166210
# mutation1 14  1 3  114  166213
nonsynonymous SNV1 14    3  82  115110
synonymous SNV      1    32   5113
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
chr11:125488282p.L505I,STT3A2
chr11:125484098p.F207F,STT3A1
chr11:125475577p.R345H,STT3A1
chr11:125478146p.A76A,STT3A1
chr11:125482500p.S209S,STT3A1
chr11:125472272p.S350I,STT3A1
chr11:125484229p.L80L,STT3A1
chr11:125476198p.V210I,STT3A1
chr11:125478178p.A365T,STT3A1
chr11:125482587p.A5S,STT3A1

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 STT3A 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 STT3A

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

ALG9,ARCN1,C11orf57,CHEK1,DDX10,DDX6,DLAT,
DPAGT1,EI24,HYOU1,PUS3,RBM7,REXO2,RNF214,
SDHD,SRPR,STT3A,UBE4A,USP28,ZPR1,ZW10
ACTL6A,ALDH18A1,AP2B1,B3GALNT1,RHNO1,VWA9,CASP2,
GANAB,HSP90B1,PDIA3,PDIA3P1,RBBP4,RDH11,SEC23B,
SHQ1,SLC39A9,STT3A,TCTN1,TCTN3,TM9SF2,XRCC5

ALG9,ARCN1,CANX,CHEK1,DPAGT1,EI24,FEN1,
GANAB,HSP90B1,HYOU1,LOC653566,NCAPD3,OSBP,POLD3,
SPCS2,SSR1,SSRP1,STIP1,STT3A,USP28,ZW10
ASCC3,ATAD2,BUB1B,CAPRIN1,DPAGT1,DTL,HSP90B1,
HYOU1,LMNB1,MESDC2,MTHFD1,PDIA4,RPN2,RRM1,
SCFD2,SEC61A1,SND1,SSRP1,STT3A,STT3B,UGGT1
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 STT3A


There's no related Drug.
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Cross referenced IDs for STT3A
* 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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