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 SEC11A
Basic gene info.Gene symbolSEC11A
Gene nameSEC11 homolog A (S. cerevisiae)
Synonyms1810012E07Rik|SEC11L1|SPC18|SPCS4A|sid2895
CytomapUCSC genome browser: 15q25.3
Genomic locationchr15 :85212774-85259674
Type of geneprotein-coding
RefGenesNM_001271918.1,
NM_001271919.1,NM_001271920.1,NM_001271921.1,NM_001271922.1,
NM_014300.3,NR_073518.1,
Ensembl idENSG00000140612
DescriptionSEC11-like protein 1SPase 18 kDa subunitendopeptidase SP18microsomal signal peptidase 18 kDa subunitsignal peptidase complex (18kD)signal peptidase complex catalytic subunit SEC11A
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000140612
HPRD : 07503
Vega : OTTHUMG00000172489
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SEC11A
BioGPS: 23478
Gene Expression Atlas: ENSG00000140612
The Human Protein Atlas: ENSG00000140612
PathwayNCI Pathway Interaction Database: SEC11A
KEGG: SEC11A
REACTOME: SEC11A
ConsensusPathDB
Pathway Commons: SEC11A
MetabolismMetaCyc: SEC11A
HUMANCyc: SEC11A
RegulationEnsembl's Regulation: ENSG00000140612
miRBase: chr15 :85,212,774-85,259,674
TargetScan: NM_001271918
cisRED: ENSG00000140612
ContextiHOP: SEC11A
cancer metabolism search in PubMed: SEC11A
UCL Cancer Institute: SEC11A
Assigned class in ccmGDBC

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Phenotypic Information for SEC11A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SEC11A
Familial Cancer Database: SEC11A
* 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_INTEGRATION_OF_ENERGY_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SEC11A
MedGen: SEC11A (Human Medical Genetics with Condition)
ClinVar: SEC11A
PhenotypeMGI: SEC11A (International Mouse Phenotyping Consortium)
PhenomicDB: SEC11A

Mutations for SEC11A
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 SEC11A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF094407VAPA131211899543199954428SEC11A120348158522394685230966
AI954648SEC11A1124158522474585224868NFIA12144416172419661724519

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       1        
GAIN (# sample)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=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
chr15:85213257-85213257p.R178H1

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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
# sample    1 1 1  1 1  11 2
# mutation    1 1 1  1 1  11 2
nonsynonymous SNV      1 1  1 1     1
synonymous SNV    1           11 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
chr15:85213257p.R138H,SEC11A1
chr15:85213986p.T113T,SEC11A1
chr15:85223960p.V89L,SEC11A1
chr15:85224008p.R73R,SEC11A1
chr15:85230875p.V98L,SEC11A1
chr15:85230906p.I87M,SEC11A1
chr15:85230953p.R72R,SEC11A1
chr15:85230968p.L67F,SEC11A1
chr15:85234816p.K37K,SEC11A1

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 SEC11A 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 SEC11A

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

AMELX,FAM103A1,KERA,LOC388152,MESDC2,MORF4L1,MRPL46,
MRPS11,PPIB,PSMA4,RPL4,RPLP1,RPS17,SCX,
SEC11A,VIMP,TM2D3,TMEFF2,TNMD,WDR73,ZNF592
ADH5,ATP5E,EMC7,TMEM256,SMIM7,C1orf123,CCDC23,
CDKN1C,COX7A2,DRAM2,GTF2E2,HEBP2,IAH1,NFU1,
RNF130,RWDD1,SEC11A,SERPINB6,STX8,EMC3,VIM

ADPGK,EMC7,COPS2,FAM103A1,FAM96A,FBXO22,KIAA0101,
MORF4L1,MRPL46,MRPS11,NOP10,PSMA4,RAB11A,RCN2,
RPS17,RSL24D1,SEC11A,SRP14,EMC4,ZFAND6,ZWILCH
BTF3,C12orf57,TIMMDC1,TMEM261,CLNS1A,DPH5,DPY30,
NAA20,NUDCD2,RPF1,RPL27A,RPL41,RPS3A,RPS6,
RPS8,RPSA,RPSAP58,SEC11A,SSR2,TBPL1,UFC1
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 SEC11A


There's no related Drug.
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Cross referenced IDs for SEC11A
* 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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