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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SEC61A2 |
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Phenotypic Information for SEC61A2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SEC61A2 |
Familial Cancer Database: SEC61A2 |
* 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_PROTEINS |
Mutations for SEC61A2 |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | SEC61A2 | chr10 | 12175105 | 12175125 | chr10 | 11417442 | 11417462 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SEC61A2 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 |
BE618201 | SEC61A2 | 1 | 181 | 10 | 12208251 | 12208431 | SEC61A2 | 179 | 618 | 10 | 12207842 | 12208283 | |
BU902594 | SEC61A2 | 34 | 130 | 10 | 12206309 | 12206405 | SEC61A2 | 123 | 398 | 10 | 12206414 | 12206689 |
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 |   |   |   |   |   |   | |||
GAIN (# sample) | 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=32) | (# total SNVs=11) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr10:12191690-12191690 | p.P106L | 3 |
chr10:12191875-12191875 | p.G126V | 3 |
chr10:12185169-12185169 | p.M65I | 2 |
chr10:12197867-12197867 | p.T185P | 2 |
chr10:12191664-12191664 | p.A97A | 2 |
chr10:12199030-12199030 | p.A247A | 2 |
chr10:12199913-12199913 | p.R262C | 2 |
chr10:12191933-12191933 | p.A145A | 2 |
chr10:12199961-12199961 | p.S278G | 1 |
chr10:12203118-12203118 | p.D389Y | 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 |   | 2 | 5 |   |   | 3 |   | 1 |   |   | 4 | 1 | 1 |   |   | 8 | 2 |   | 4 |
# mutation | 1 |   | 2 | 5 |   |   | 3 |   | 1 |   |   | 3 | 1 | 1 |   |   | 10 | 2 |   | 4 |
nonsynonymous SNV |   |   | 2 | 4 |   |   | 2 |   | 1 |   |   | 3 | 1 | 1 |   |   | 7 | 1 |   | 3 |
synonymous SNV | 1 |   |   | 1 |   |   | 1 |   |   |   |   |   |   |   |   |   | 3 | 1 |   | 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 |
chr10:12191875 | p.G104V,SEC61A2 | 2 |
chr10:12204267 | p.A311T,SEC61A2 | 1 |
chr10:12191670 | p.Y115N,SEC61A2 | 1 |
chr10:12199961 | p.S354C,SEC61A2 | 1 |
chr10:12206306 | p.E120K,SEC61A2 | 1 |
chr10:12199962 | p.D367Y,SEC61A2 | 1 |
chr10:12206337 | p.L138L,SEC61A2 | 1 |
chr10:12191907 | p.L372L,SEC61A2 | 1 |
chr10:12199963 | p.G156W,SEC61A2 | 1 |
chr10:12206359 | p.S386Y,SEC61A2 | 1 |
Other DBs for Point Mutations |
Copy Number for SEC61A2 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 SEC61A2 |
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 |
C10orf111,CCDC150,CDC123,CENPE,DCLRE1C,DHTKD1,ESPL1, HSPA14,KIF18B,KIN,MCM10,NCAPG,NUDT5,PRPF18, RBM17,SEC61A2,SEPHS1,SKA1,SUV39H2,UBE2C,UPF2 | ANKRD26,C17orf75,C18orf25,TYW5,TRMT13,DYRK1A,METTL15, NAA15,NAA25,NAA35,NUPL1,OTUD6B,PARG,RAD1, RPAP3,SEC61A2,THAP9,TPP2,YTHDC2,ZBTB11,ZBTB43 |
AGAP4,AGAP6,FAM208B,CATSPER2,CCDC150,CCDC84,DCLRE1C, DDX12P,FBXO18,GTPBP4,KCTD19,KIAA0907,PABPC1L,PASK, RBM17,SCARNA12,SEC61A2,SNORA8,SUZ12P1,TMEM194A,ZNF767P | ARIH2,ARSJ,CCP110,DGKE,DNAJC27,EPHA3,EPM2AIP1, INTU,LOC646851,LUC7L3,POFUT2,TRMT10B,RUFY2,SEC61A2, SEPT7P2,SRSF11,PNISR,SUZ12P1,TMX3,ZMAT1,ZNF354B |
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 SEC61A2 |
There's no related Drug. |
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Cross referenced IDs for SEC61A2 |
* 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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