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 SEH1L
Basic gene info.Gene symbolSEH1L
Gene nameSEH1-like (S. cerevisiae)
SynonymsSEC13L|SEH1A|SEH1B|Seh1
CytomapUCSC genome browser: 18p11.21
Genomic locationchr18 :12947982-12987536
Type of geneprotein-coding
RefGenesNM_001013437.1,
NM_031216.3,
Ensembl idENSG00000085415
Descriptionnucleoporin SEH1nup107-160 subcomplex subunit SEH1sec13 like proteinsec13-like protein
Modification date20141207
dbXrefs MIM : 609263
HGNC : HGNC
Ensembl : ENSG00000085415
HPRD : 15319
Vega : OTTHUMG00000181909
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SEH1L
BioGPS: 81929
Gene Expression Atlas: ENSG00000085415
The Human Protein Atlas: ENSG00000085415
PathwayNCI Pathway Interaction Database: SEH1L
KEGG: SEH1L
REACTOME: SEH1L
ConsensusPathDB
Pathway Commons: SEH1L
MetabolismMetaCyc: SEH1L
HUMANCyc: SEH1L
RegulationEnsembl's Regulation: ENSG00000085415
miRBase: chr18 :12,947,982-12,987,536
TargetScan: NM_001013437
cisRED: ENSG00000085415
ContextiHOP: SEH1L
cancer metabolism search in PubMed: SEH1L
UCL Cancer Institute: SEH1L
Assigned class in ccmGDBC

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Phenotypic Information for SEH1L(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SEH1L
Familial Cancer Database: SEH1L
* 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_NON_CODING_RNA
REACTOME_METABOLISM_OF_RNA
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SEH1L
MedGen: SEH1L (Human Medical Genetics with Condition)
ClinVar: SEH1L
PhenotypeMGI: SEH1L (International Mouse Phenotyping Consortium)
PhenomicDB: SEH1L

Mutations for SEH1L
* 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 SEH1L related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE772602SEH1L15277181298644812986710MTCH127435863693901136939095
AA559852SEH1L1144181298738912987531SEH1L129339181298722912987439

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    1   1    
GAIN (# sample)   1    1   1    
LOSS (# sample)                 
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr18:12955467-12955467p.H56H5
chr18:12971157-12971157p.R176H2
chr18:12987007-12987007p.R406L2
chr18:12982560-12982560p.H269Y2
chr18:12963339-12963339p.S164R1
chr18:12982630-12982630p.V292A1
chr18:12955531-12955531p.S78T1
chr18:12986964-12986964p.D392N1
chr18:12948130-12948130p.A4T1
chr18:12984076-12984076p.L319F1

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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
# sample11 2    1  41   44 5
# mutation11 2    1  41   34 6
nonsynonymous SNV 1 1    1  21   34 5
synonymous SNV1  1       2       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
chr18:12982560p.H269Y,SEH1L2
chr18:12984133p.G261C,SEH1L1
chr18:12963339p.I7I,SEH1L1
chr18:12984160p.V292A,SEH1L1
chr18:12948141p.A28T,SEH1L1
chr18:12971157p.L319F,SEH1L1
chr18:12986900p.A51T,SEH1L1
chr18:12948202p.N336T,SEH1L1
chr18:12971215p.S52R,SEH1L1
chr18:12986964p.P337S,SEH1L1

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 SEH1L 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 SEH1L

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

AFG3L2,FAM210A,CEP192,CEP76,L3MBTL4,METTL4,NDC80,
PSMG2,PTPN2,PUS7,RAB12,RNF138,RNMT,SEH1L,
SNRPD1,SRPK1,TAF4B,TYMS,UBA2,WDR12,YES1
ABCE1,AMD1,API5,MZT1,C5orf28,CBX3,DIMT1,
EIF4E,MAK16,MTPAP,NUS1,PTGES3,RAB14,TRMT10C,
RNF138,RWDD4,SCOC,SEH1L,SLMO2,TIPRL,TWISTNB

AFG3L2,FAM210A,CEP76,METTL4,MYL12A,MYL12B,NAPG,
NDC80,NDUFV2,PSMG2,PTPN2,RALBP1,RNF138,RNMT,
SEH1L,SNRPD1,THOC1,TYMS,USP14,VAPA,YES1
ABCE1,AGPAT5,FAM210A,DDX21,EIF3J,FASTKD2,GRPEL1,
MARS2,NIFK,NDUFAF4,NOL10,NOP16,PIGW,RCL1,
TRMT10C,SEH1L,SLC25A17,SRFBP1,TRMT6,UMPS,WDR43
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 SEH1L


There's no related Drug.
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Cross referenced IDs for SEH1L
* 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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