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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SEH1L |
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Phenotypic Information for SEH1L(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SEH1L |
Familial Cancer Database: SEH1L |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA REACTOME_METABOLISM_OF_CARBOHYDRATES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: SEH1L |
MedGen: SEH1L (Human Medical Genetics with Condition) | |
ClinVar: SEH1L | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SEH1L related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BE772602 | SEH1L | 15 | 277 | 18 | 12986448 | 12986710 | MTCH1 | 274 | 358 | 6 | 36939011 | 36939095 | |
AA559852 | SEH1L | 1 | 144 | 18 | 12987389 | 12987531 | SEH1L | 129 | 339 | 18 | 12987229 | 12987439 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=27) | (# total SNVs=11) |
(# total SNVs=0) | (# total SNVs=1) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr18:12955467-12955467 | p.H56H | 5 |
chr18:12982560-12982560 | p.H269Y | 2 |
chr18:12971157-12971157 | p.R176H | 2 |
chr18:12987007-12987007 | p.R406L | 2 |
chr18:12971180-12971180 | p.V184I | 1 |
chr18:12948141-12948141 | p.I7I | 1 |
chr18:12984110-12984110 | p.Q331* | 1 |
chr18:12955608-12955608 | p.W103C | 1 |
chr18:12987030-12987030 | p.P414S | 1 |
chr18:12971215-12971215 | p.A195A | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 1 |   | 2 |   |   |   |   | 1 |   |   | 4 | 1 |   |   |   | 4 | 4 |   | 5 |
# mutation | 1 | 1 |   | 2 |   |   |   |   | 1 |   |   | 4 | 1 |   |   |   | 3 | 4 |   | 6 |
nonsynonymous SNV |   | 1 |   | 1 |   |   |   |   | 1 |   |   | 2 | 1 |   |   |   | 3 | 4 |   | 5 |
synonymous SNV | 1 |   |   | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr18:12982560 | p.H269Y,SEH1L | 2 |
chr18:12986900 | p.A51T,SEH1L | 1 |
chr18:12948202 | p.N336T,SEH1L | 1 |
chr18:12971215 | p.S52R,SEH1L | 1 |
chr18:12986964 | p.P337S,SEH1L | 1 |
chr18:12951893 | p.S57G,SEH1L | 1 |
chr18:12982531 | p.S338S,SEH1L | 1 |
chr18:12987007 | p.V60V,SEH1L | 1 |
chr18:12951898 | p.Q347Q,SEH1L | 1 |
chr18:12982536 | p.A66T,SEH1L | 1 |
Other DBs for Point Mutations |
Copy 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 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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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 |
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