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 SEC61A1
Basic gene info.Gene symbolSEC61A1
Gene nameSec61 alpha 1 subunit (S. cerevisiae)
SynonymsHSEC61|SEC61|SEC61A
CytomapUCSC genome browser: 3q21.3
Genomic locationchr3 :127771211-127790526
Type of geneprotein-coding
RefGenesNM_013336.3,
Ensembl idENSG00000058262
DescriptionSec61 alpha-1protein transport protein SEC61 alpha subunitprotein transport protein Sec61 subunit alphaprotein transport protein Sec61 subunit alpha isoform 1sec61 homolog
Modification date20141207
dbXrefs MIM : 609213
HGNC : HGNC
Ensembl : ENSG00000058262
HPRD : 15316
Vega : OTTHUMG00000159624
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SEC61A1
BioGPS: 29927
Gene Expression Atlas: ENSG00000058262
The Human Protein Atlas: ENSG00000058262
PathwayNCI Pathway Interaction Database: SEC61A1
KEGG: SEC61A1
REACTOME: SEC61A1
ConsensusPathDB
Pathway Commons: SEC61A1
MetabolismMetaCyc: SEC61A1
HUMANCyc: SEC61A1
RegulationEnsembl's Regulation: ENSG00000058262
miRBase: chr3 :127,771,211-127,790,526
TargetScan: NM_013336
cisRED: ENSG00000058262
ContextiHOP: SEC61A1
cancer metabolism search in PubMed: SEC61A1
UCL Cancer Institute: SEC61A1
Assigned class in ccmGDBC

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Phenotypic Information for SEC61A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SEC61A1
Familial Cancer Database: SEC61A1
* 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: SEC61A1
MedGen: SEC61A1 (Human Medical Genetics with Condition)
ClinVar: SEC61A1
PhenotypeMGI: SEC61A1 (International Mouse Phenotyping Consortium)
PhenomicDB: SEC61A1

Mutations for SEC61A1
* 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 SEC61A1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF959743DIDO114368206153860361541296SEC61A13604313127789080127789151
AW105324SEC61A111933127790242127790434CCT519031551026266210263302
DA769011SNHG1166116262248662622551SEC61A1665183127785924127788431
DA580258ZC3H11A11551203764776203764930SEC61A11565623127775637127783815
AA405428SEC61A1411493127787546127787654SEC61A11443923127788221127788468
AW939919SEC61A111363127789016127789152SEC61A11192233127789165127789271
AW897979GUCY1A3124884156653270156653746SEC61A14786363127788885127789044
BE835544UBTF1278174228580842286084SEC61A12754323127789422127789579
BF748943SEC61A1162533127789430127789668SEC61A12475963127788923127789272

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          
GAIN (# sample)                 
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=33)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr3:127783794-127783794p.R231W2
chr3:127783795-127783795p.R231Q2
chr3:127785825-127785825p.S269L2
chr3:127788458-127788458p.V462I2
chr3:127783746-127783746p.A215T2
chr3:127786902-127786902p.R415L2
chr3:127783771-127783771p.R223H2
chr3:127779411-127779411p.L175I2
chr3:127786281-127786281p.G331G1
chr3:127774381-127774381p.L33P1

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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 2 9  3 1  422 135 4
# mutation 2 8  3 1  522 136 4
nonsynonymous SNV 2 8  2    422 112 4
synonymous SNV      1 1  1    24  
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
chr3:127783746p.A215T3
chr3:127788458p.S269L2
chr3:127783795p.V462I2
chr3:127785825p.R415Q2
chr3:127786902p.R231L2
chr3:127788428p.T452A1
chr3:127774381p.L33P1
chr3:127783766p.T286M1
chr3:127786337p.F51Y1
chr3:127774526p.G80E1

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 SEC61A1 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 SEC61A1

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

ACAD9,AP2M1,TIMMDC1,HMCES,CALR,COPB2,COPG1,
DDOST,DNAJB11,HSP90B1,HYOU1,ISY1,P4HB,PDIA4,
PDIA5,PDIA6,RPN1,SEC61A1,SRPRB,TMEM214,TMEM39A
AP1B1,CALR,CHPF2,CHPF,CKAP4,CNDP2,DDOST,
GMPPB,HSPA5,HYOU1,P4HB,PDIA3P1,PDIA4,PDIA6,
RPN1,RUVBL1,SEC61A1,SEPT9,SRPRB,ST14,YARS

CKAP4,COPB2,COPG1,DNAJC3,EIF4G1,GLG1,GMPPA,
HDLBP,HSPA5,HYOU1,NUCB2,P4HB,PDIA5,RPN1,
SEC24D,SEC61A1,SLC39A7,SSR3,SURF4,TMED9,TMEM214
COPG1,EFTUD2,HIRA,HNRNPM,HYOU1,LMNB2,LOC401010,
MED24,MTA2,MYO1B,NCLN,PDIA4,PTBP1,RPN2,
SEC61A1,SLC5A6,STT3A,TMEM104,TMEM214,UGGT1,VARS
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 SEC61A1


There's no related Drug.
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Cross referenced IDs for SEC61A1
* 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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