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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SEC24B |
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Phenotypic Information for SEC24B(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SEC24B |
Familial Cancer Database: SEC24B |
* 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 |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: SEC24B |
MedGen: SEC24B (Human Medical Genetics with Condition) | |
ClinVar: SEC24B | |
Phenotype | MGI: SEC24B (International Mouse Phenotyping Consortium) |
PhenomicDB: SEC24B |
Mutations for SEC24B |
* 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 SEC24B 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 |
AV726458 | SEC24B | 1 | 530 | 4 | 110384093 | 110384622 | MALAT1 | 526 | 685 | 11 | 65270650 | 65270813 | |
AV715572 | SEC24B | 1 | 457 | 4 | 110450428 | 110450882 | SEC24B | 456 | 560 | 4 | 110449940 | 110450044 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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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=78) | (# total SNVs=26) |
(# total SNVs=1) | (# 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 |
chr4:110384109-110384109 | p.Q62Q | 3 |
chr4:110384361-110384361 | p.T146T | 3 |
chr4:110437770-110437770 | p.C665C | 2 |
chr4:110415851-110415851 | p.S408P | 2 |
chr4:110441545-110441545 | p.R682T | 2 |
chr4:110431172-110431172 | p.R526W | 2 |
chr4:110415985-110415985 | p.V452V | 2 |
chr4:110441582-110441582 | p.F694L | 2 |
chr4:110442694-110442694 | p.R772H | 2 |
chr4:110441604-110441604 | p.S702P | 2 |
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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 | 3 | 6 |   | 17 | 3 |   | 5 |   | 2 | 1 |   | 10 | 4 | 2 |   | 1 | 8 | 14 |   | 13 |
# mutation | 4 | 6 |   | 16 | 3 |   | 5 |   | 2 | 1 |   | 14 | 4 | 2 |   | 1 | 8 | 15 |   | 14 |
nonsynonymous SNV | 2 | 3 |   | 13 | 1 |   | 4 |   | 2 | 1 |   | 7 | 3 | 1 |   | 1 | 2 | 10 |   | 11 |
synonymous SNV | 2 | 3 |   | 4 | 2 |   | 1 |   |   |   |   | 7 | 1 | 1 |   |   | 6 | 5 |   | 3 |
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 |
chr4:110442694 | p.R772H,SEC24B | 2 |
chr4:110448544 | p.A976V,SEC24B | 2 |
chr4:110431204 | p.Q536H,SEC24B | 2 |
chr4:110459743 | p.G771G,SEC24B | 1 |
chr4:110384141 | p.L940V,SEC24B | 1 |
chr4:110415933 | p.H1193Y,SEC24B | 1 |
chr4:110442693 | p.Q306Q,SEC24B | 1 |
chr4:110384778 | p.T430R,SEC24B | 1 |
chr4:110431225 | p.T563A,SEC24B | 1 |
chr4:110447419 | p.R772G,SEC24B | 1 |
Other DBs for Point Mutations |
Copy Number for SEC24B 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 SEC24B |
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 |
BOD1L1,C4orf29,TRAPPC11,CLCN3,CLOCK,DNAJB14,DPP8, KIAA1109,CFAP97,LIN54,METTL14,REST,RNF111,SEC24B, SMARCAD1,TET2,TMEM184C,UBE2D3,UBR3,USP38,WDFY3 | ARIH1,ATRX,TRAPPC11,CAPN7,COG5,TRAPPC8,KIAA2026, KRIT1,MORC3,RAB3GAP2,LTN1,RPS6KB1,SEC24B,SCAF11, SKIV2L2,SP1,STAG2,TAB2,USP8,ZFX,ZNF280D |
AFF1,ANKRD17,AP1AR,TRAPPC11,CLCN3,DNAJB14,G3BP2, HERC3,KIAA1109,LRBA,METTL14,OTUD4,SEC24B,SH3D19, SMAD1,SMARCA5,TMEM184C,UBE2D3,USP38,USP53,WDFY3 | ANKHD1,ARID2,CLTC,CNOT1,CSNK2A1,CTCF,DDX6, DLG1,GAPVD1,GNAQ,MAPK1,MED13,OSBPL11,PAFAH1B1, PHF3,RALGAPB,RNF111,SEC24B,SEL1L,SCAF11,USP9X |
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 SEC24B |
There's no related Drug. |
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Cross referenced IDs for SEC24B |
* 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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