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 SEC31A
Basic gene info.Gene symbolSEC31A
Gene nameSEC31 homolog A (S. cerevisiae)
SynonymsABP125|ABP130|HSPC334|SEC31L1
CytomapUCSC genome browser: 4q21.22
Genomic locationchr4 :83739813-83812412
Type of geneprotein-coding
RefGenesNM_001077206.2,
NM_001077207.2,NM_001077208.2,NM_001191049.1,NM_001300744.1,
NM_001300745.1,NM_014933.3,NM_016211.3,
Ensembl idENSG00000138674
DescriptionSEC31-like protein 1SEC31-related protein Aprotein transport protein Sec31Aweb1-like proteinyeast Sec31p homolog
Modification date20141222
dbXrefs MIM : 610257
HGNC : HGNC
Ensembl : ENSG00000138674
HPRD : 15314
Vega : OTTHUMG00000130297
ProteinUniProt: O94979
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SEC31A
BioGPS: 22872
Gene Expression Atlas: ENSG00000138674
The Human Protein Atlas: ENSG00000138674
PathwayNCI Pathway Interaction Database: SEC31A
KEGG: SEC31A
REACTOME: SEC31A
ConsensusPathDB
Pathway Commons: SEC31A
MetabolismMetaCyc: SEC31A
HUMANCyc: SEC31A
RegulationEnsembl's Regulation: ENSG00000138674
miRBase: chr4 :83,739,813-83,812,412
TargetScan: NM_001077206
cisRED: ENSG00000138674
ContextiHOP: SEC31A
cancer metabolism search in PubMed: SEC31A
UCL Cancer Institute: SEC31A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for SEC31A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SEC31A
Familial Cancer Database: SEC31A
* 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 610257; gene.
610257; gene.
Orphanet
DiseaseKEGG Disease: SEC31A
MedGen: SEC31A (Human Medical Genetics with Condition)
ClinVar: SEC31A
PhenotypeMGI: SEC31A (International Mouse Phenotyping Consortium)
PhenomicDB: SEC31A

Mutations for SEC31A
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastSEC31Achr48374502283745022chr89825084298250842
breastSEC31Achr48374513783745137PTDSS1chr89733652197336521
ovarySEC31Achr48374948183749501SCD5chr48367776683677786
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SEC31A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI052970SEC31A131748376555683770072LRCH43173747100174335100174392
DT220653SMC1A1218X5344943953449656SEC31A21639748374866483750212
BM992139SEC31A842648374016483745811ARPC54226721183602237183604849
BI823499SEC31A145948379988183812291PTEN456804108972504289725387
CA419101MTA326330624273131842731361SEC31A30569448376813783768533
BF751621SEC31A4442748381917483821677MEMO141248623209498332108490
AV746752SEC31A16148374121083741270SEC31A5839348374209283742435
AI523884SEC31A320548381416283814364FUBP120054317844324178443584
BF839137CTPS2172304X1667256116672693SEC31A29850548380361883803824
DT219678SMC1A1218X5344943953449656SEC31A21665948374570883750212
BF824998CD101243701117576519117576864SEC31A36649148374010283740227
BP418474SEC31A1410348374159183741680ARFGAP1103439206191944861919784
DB231724PHF151945133860086133860179SEC31A9455548379988383812295
AF161393SEC31A1156248373981483765613BCKDHB1559157868086555780865576
CR933696SEC31A1368748373981483812306BCKDHB3684370368086555780865576
AL049463SEC31A157148373981483740384PPP2R2C562587464106026410627
AF161452SEC31A1138248373981483763567BCKDHB1379139868086555780865576

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 # sample1            11  
GAIN (# sample)1                
LOSS (# sample)             11  
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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=1)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
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
chr4:83778206-83778206p.R555C1

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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
# sample34 121 6 5  1163 1710 14
# mutation34 121 6 5  1263 1710 18
nonsynonymous SNV14 71 5 1  1062  46 12
synonymous SNV2  5  1 4  2 1 134 6
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
chr4:83763465p.R744C,SEC31A2
chr4:83770112p.A893A,SEC31A2
chr4:83748592p.S1002L,SEC31A1
chr4:83774850p.R855Q,SEC31A1
chr4:83795793p.I601V,SEC31A1
chr4:83763338p.L378L,SEC31A1
chr4:83778873p.A180T,SEC31A1
chr4:83801963p.Q999R,SEC31A1
chr4:83770026p.P830T,SEC31A1
chr4:83788320p.I590I,SEC31A1

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 SEC31A 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 SEC31A

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

ADAMTS12,ANXA5,ARCN1,ENTPD7,FAM114A1,FBN1,ITGAV,
LIN54,PRRC1,SEC23A,SEC24A,SEC24B,SEC24D,SEC31A,
SLAIN2,SLC10A7,TBC1D8B,TCF12,TJP1,USO1,VCAN
AGFG1,AGPS,AHCYL1,AP3M1,ARCN1,ARHGAP21,CALU,
CDC27,CLTC,EXOC5,GNG12,HGSNAT,LUZP6,RABL3,
SEC22B,SEC31A,SLC35B4,TMEM167A,VAMP7,CHMP3,XPOT

ANTXR1,ARHGAP1,BMPR2,EHD2,FBXL7,FIBIN,FKBP7,
FSTL1,FZD1,ITGAV,LAMA4,LAMC1,LTBP1,SEC31A,
SGCD,SNX18,SPOCK1,SSPN,TCF4,TIMP2,TSHZ3
AHCYL1,ALS2,ARID1B,BAZ2B,CEP120,CREB3L2,FAM168A,
FBXW2,GIGYF2,GIT2,GTF2IP1,MAPKBP1,NBAS,NFATC3,
PCM1,PCNX,SEC31A,SMC3,UBR1,ZNF106,ZNF507
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 SEC31A


There's no related Drug.
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Cross referenced IDs for SEC31A
* 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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