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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) |
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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/ |
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REACTOME_METABOLISM_OF_PROTEINS |
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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. |
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There's no structural variation information in COSMIC data for this gene. |
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* 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 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=78) | (# total SNVs=26) |
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(# total SNVs=1) | (# total SNVs=1) |
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* 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 |
chr4:110433113-110433113 | p.Q558* | 2 |
chr4:110447419-110447419 | p.V908V | 2 |
chr4:110415930-110415930 | p.G434D | 2 |
chr4:110433153-110433153 | p.R571Q | 2 |
chr4:110451548-110451548 | p.L1025F | 2 |
chr4:110442602-110442602 | p.L741L | 2 |
chr4:110437770-110437770 | p.C665C | 2 |
chr4:110415851-110415851 | p.S408P | 2 |
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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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* 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 |
chr4:110431204 | p.Q536H,SEC24B | 2 |
chr4:110442694 | p.A976V,SEC24B | 2 |
chr4:110448544 | p.R772H,SEC24B | 2 |
chr4:110452662 | p.L829V,SEC24B | 1 |
chr4:110415906 | p.T1054T,SEC24B | 1 |
chr4:110442579 | p.H249Q,SEC24B | 1 |
chr4:110384653 | p.P404S,SEC24B | 1 |
chr4:110427571 | p.R526W,SEC24B | 1 |
chr4:110445995 | p.C665C,SEC24B | 1 |
chr4:110402835 | p.R892M,SEC24B | 1 |
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* 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. |
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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 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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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 |
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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 |
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* 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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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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