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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SEC23A |
Basic gene info. | Gene symbol | SEC23A |
Gene name | Sec23 homolog A (S. cerevisiae) | |
Synonyms | CLSD | |
Cytomap | UCSC genome browser: 14q21.1 | |
Genomic location | chr14 :39501122-39572437 | |
Type of gene | protein-coding | |
RefGenes | NM_006364.2, | |
Ensembl id | ENSG00000100934 | |
Description | SEC23-related protein Aprotein transport protein Sec23A | |
Modification date | 20141207 | |
dbXrefs | MIM : 610511 | |
HGNC : HGNC | ||
Ensembl : ENSG00000100934 | ||
HPRD : 06714 | ||
Vega : OTTHUMG00000028812 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SEC23A | |
BioGPS: 10484 | ||
Gene Expression Atlas: ENSG00000100934 | ||
The Human Protein Atlas: ENSG00000100934 | ||
Pathway | NCI Pathway Interaction Database: SEC23A | |
KEGG: SEC23A | ||
REACTOME: SEC23A | ||
ConsensusPathDB | ||
Pathway Commons: SEC23A | ||
Metabolism | MetaCyc: SEC23A | |
HUMANCyc: SEC23A | ||
Regulation | Ensembl's Regulation: ENSG00000100934 | |
miRBase: chr14 :39,501,122-39,572,437 | ||
TargetScan: NM_006364 | ||
cisRED: ENSG00000100934 | ||
Context | iHOP: SEC23A | |
cancer metabolism search in PubMed: SEC23A | ||
UCL Cancer Institute: SEC23A | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for SEC23A(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SEC23A |
Familial Cancer Database: SEC23A |
* 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: SEC23A |
MedGen: SEC23A (Human Medical Genetics with Condition) | |
ClinVar: SEC23A | |
Phenotype | MGI: SEC23A (International Mouse Phenotyping Consortium) |
PhenomicDB: SEC23A |
Mutations for SEC23A |
* 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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- Statistics for Tissue and Mutation type | Top |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | SEC23A | chr14 | 39553185 | 39553205 | SEC23A | chr14 | 39552946 | 39552966 |
pancreas | SEC23A | chr14 | 39502839 | 39502859 | SEC23A | chr14 | 39502708 | 39502728 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SEC23A 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 |
AI445956 | SEC23A | 28 | 117 | 14 | 39560265 | 39560358 | NUP107 | 116 | 140 | 12 | 69083941 | 69083966 | |
AA057305 | SEC23A | 1 | 154 | 14 | 39533179 | 39533332 | ARL11 | 152 | 335 | 13 | 50205498 | 50205681 | |
AA774945 | STEAP2 | 2 | 159 | 7 | 89863607 | 89863764 | SEC23A | 160 | 324 | 14 | 39524422 | 39531055 | |
F00808 | SEC23A | 106 | 174 | 14 | 39501988 | 39502056 | SEC23A | 175 | 318 | 14 | 39524347 | 39524489 | |
BQ647036 | SEC23A | 1 | 63 | 14 | 39572252 | 39572314 | OSER1 | 58 | 893 | 20 | 42826157 | 42839097 | |
D44754 | SEC23A | 1 | 83 | 14 | 39560272 | 39560356 | SNRNP200 | 70 | 165 | 2 | 96965108 | 96966773 | |
BE072523 | SEC23A | 12 | 93 | 14 | 39561352 | 39561435 | NR6A1 | 85 | 435 | 9 | 127366382 | 127366732 | |
D82153 | SEC23A | 2 | 390 | 14 | 39502269 | 39509996 | SEC23A | 384 | 452 | 14 | 39501988 | 39502056 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   |   |   | 2 |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   | 2 |   |   |   |   |   |   |   |   | |||
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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Stat. for Non-Synonymous SNVs (# total SNVs=57) | (# total SNVs=13) |
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(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr14:39514391-39514391 | p.A625A | 3 |
chr14:39512066-39512066 | p.L637P | 3 |
chr14:39517925-39517925 | p.K556K | 2 |
chr14:39565270-39565270 | p.R18Q | 2 |
chr14:39565272-39565272 | p.V17V | 2 |
chr14:39524447-39524447 | p.E520V | 2 |
chr14:39536469-39536469 | p.T379A | 2 |
chr14:39565308-39565308 | p.L5F | 2 |
chr14:39502513-39502513 | p.L743H | 2 |
chr14:39565189-39565189 | p.L45P | 1 |
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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 |   | 12 |   |   | 2 |   | 2 | 1 |   | 8 | 2 | 4 |   |   | 6 | 6 | 1 | 4 |
# mutation | 1 | 2 |   | 11 |   |   | 2 |   | 2 | 1 |   | 8 | 2 | 4 |   |   | 7 | 8 | 1 | 7 |
nonsynonymous SNV | 1 | 2 |   | 6 |   |   | 1 |   | 2 | 1 |   | 7 | 2 | 4 |   |   | 6 | 4 |   | 7 |
synonymous SNV |   |   |   | 5 |   |   | 1 |   |   |   |   | 1 |   |   |   |   | 1 | 4 | 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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* 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 |
chr14:39512066 | p.L637P | 3 |
chr14:39536469 | p.L5L | 2 |
chr14:39565308 | p.T379A | 2 |
chr14:39514489 | p.E6K | 1 |
chr14:39560913 | p.T708I | 1 |
chr14:39532596 | p.I513T | 1 |
chr14:39509955 | p.P298L | 1 |
chr14:39545233 | p.L685L | 1 |
chr14:39517897 | p.T497I | 1 |
chr14:39565170 | p.A267T | 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 SEC23A |
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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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ADAM12,ADAMTS12,ANTXR1,BICC1,C14orf37,CDH11,COL5A2, COL6A3,DACT1,FAM26E,FAP,FBN1,FERMT2,FSTL1, LOX,MXRA5,NID2,SEC23A,THBS2,VCAN,ZEB1 | ABCC9,ANKRD40,ASPA,BCAP29,CALM1,DIAPH2,FAM92A1, FOXN3,QKI,RAD23B,RTN4,SEC23A,SETD7,SGCB, SH3GLB1,TTC7B,UGP2,YPEL2,YWHAG,ZEB1,ZFPM2 |
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BAZ1A,DPP8,EXOC5,GMFB,GNA13,GUCY1B3,HEATR5A, ITGAV,ITGB3,KLHL28,LPP,MAP4K5,MGAT2,MPP5, PCNX,SEC23A,SEL1L,SNX6,SOCS4,SRP54,TRAPPC6B | ACTB,ACTR1A,AKTIP,C6orf106,CALM1,CDC42EP4,EFR3A, FEZ2,HNRNPH2,INPP5A,KPNA1,LARGE,MBNL1,MFN2, NRBP1,PDK3,RPS6KA5,SEC23A,SERINC1,SLC9A6,UBE2G1 |
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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 SEC23A |
There's no related Drug. |
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Cross referenced IDs for SEC23A |
* 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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