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 SEC61B
Basic gene info.Gene symbolSEC61B
Gene nameSec61 beta subunit
Synonyms-
CytomapUCSC genome browser: 9q22.32-q31.3
Genomic locationchr9 :101984569-101992901
Type of geneprotein-coding
RefGenesNM_006808.2,
Ensembl idENSG00000106803
DescriptionSec61 complex, beta subunitprotein translocation complex betaprotein transport protein SEC61 beta subunitprotein transport protein Sec61 subunit beta
Modification date20141207
dbXrefs MIM : 609214
HGNC : HGNC
Ensembl : ENSG00000106803
HPRD : 06715
Vega : OTTHUMG00000020354
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SEC61B
BioGPS: 10952
Gene Expression Atlas: ENSG00000106803
The Human Protein Atlas: ENSG00000106803
PathwayNCI Pathway Interaction Database: SEC61B
KEGG: SEC61B
REACTOME: SEC61B
ConsensusPathDB
Pathway Commons: SEC61B
MetabolismMetaCyc: SEC61B
HUMANCyc: SEC61B
RegulationEnsembl's Regulation: ENSG00000106803
miRBase: chr9 :101,984,569-101,992,901
TargetScan: NM_006808
cisRED: ENSG00000106803
ContextiHOP: SEC61B
cancer metabolism search in PubMed: SEC61B
UCL Cancer Institute: SEC61B
Assigned class in ccmGDBC

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Phenotypic Information for SEC61B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SEC61B
Familial Cancer Database: SEC61B
* 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: SEC61B
MedGen: SEC61B (Human Medical Genetics with Condition)
ClinVar: SEC61B
PhenotypeMGI: SEC61B (International Mouse Phenotyping Consortium)
PhenomicDB: SEC61B

Mutations for SEC61B
* 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 SEC61B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=6)
Stat. for Synonymous SNVs
(# total SNVs=2)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=1)

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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
chr9:101990236-101990236p.M55fs*222
chr9:101992659-101992659p.A82T2
chr9:101984837-101984838p.S7fs*41
chr9:101984847-101984847p.G8A1
chr9:101984916-101984916p.V31A1
chr9:101990190-101990190p.A37A1
chr9:101990194-101990194p.C39R1
chr9:101990216-101990216p.R46H1
chr9:101992699-101992699p.R95H1
chr9:101992703-101992703p.S96S1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 3  1 1        1 2
# mutation 1 2  1 1        1 2
nonsynonymous SNV   2  1 1        1 2
synonymous SNV 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
chr9:101992659p.A82T3
chr9:101992699p.R95H2
chr9:101984847p.G8A1
chr9:101990194p.C39R1
chr9:101990216p.R46H1
chr9:101992703p.S96S1

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 SEC61B 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 SEC61B

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

ATP5J2,TMEM258,C14orf2,C19orf43,C9orf142,COX4I1,COX5B,
COX6B1,EDF1,GADD45GIP1,MRPL41,NDUFA1,NDUFA8,OST4,
PPIB,RPL35,SEC61B,SHFM1,TXN,UQCR10,USMG5
ATOX1,C17orf49,C19orf43,CFL1,CLTA,FTSJ1,JTB,
KRTCAP2,MPDU1,ORMDL2,PFN1,POLR2G,PSENEN,RHOC,
SEC61B,TAF10,TMEM147,TMEM179B,TMSB10,TRAPPC1,TXNDC17

ALG2,C19orf10,CHCHD1,COPE,COX7A2,DYNLL1,DYNLT1,
EDF1,ERP44,MED27,MRPL41,MRPL50,NDUFC1,OSTC,
PPIB,PSMB7,RPL35,SEC61B,SF3B5,SSNA1,URM1
HYPK,C19orf10,GTF2E2,MAGOH,MRPL20,PDIA6,PGK1,
PPIB,PREB,PSMA1,PSMA3,PSMA5,PSMB3,PSMD13,
PSMD14,RPL22L1,RPL26L1,RPN1,SEC11C,SEC61B,SSR3
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 SEC61B


There's no related Drug.
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Cross referenced IDs for SEC61B
* 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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