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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RBM8A |
Basic gene info. | Gene symbol | RBM8A |
Gene name | RNA binding motif protein 8A | |
Synonyms | BOV-1A|BOV-1B|BOV-1C|C1DELq21.1|DEL1q21.1|MDS014|RBM8|RBM8B|TAR|Y14|ZNRP|ZRNP1 | |
Cytomap | UCSC genome browser: 1q21.1 | |
Genomic location | chr1 :145507556-145513535 | |
Type of gene | protein-coding | |
RefGenes | NM_005105.4, | |
Ensembl id | ENSG00000265241 | |
Description | BOV-1RNA binding motif protein 8BRNA-binding motif protein 8ARNA-binding protein 8ARNA-binding protein Y14binder of OVCA1-1ribonucleoprotein RBM8ribonucleoprotein RBM8A | |
Modification date | 20141219 | |
dbXrefs | MIM : 605313 | |
HGNC : HGNC | ||
Ensembl : ENSG00000265241 | ||
HPRD : 05609 | ||
Vega : OTTHUMG00000013736 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RBM8A | |
BioGPS: 9939 | ||
Gene Expression Atlas: ENSG00000265241 | ||
The Human Protein Atlas: ENSG00000265241 | ||
Pathway | NCI Pathway Interaction Database: RBM8A | |
KEGG: RBM8A | ||
REACTOME: RBM8A | ||
ConsensusPathDB | ||
Pathway Commons: RBM8A | ||
Metabolism | MetaCyc: RBM8A | |
HUMANCyc: RBM8A | ||
Regulation | Ensembl's Regulation: ENSG00000265241 | |
miRBase: chr1 :145,507,556-145,513,535 | ||
TargetScan: NM_005105 | ||
cisRED: ENSG00000265241 | ||
Context | iHOP: RBM8A | |
cancer metabolism search in PubMed: RBM8A | ||
UCL Cancer Institute: RBM8A | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for RBM8A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: RBM8A |
Familial Cancer Database: RBM8A |
* 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_MRNA REACTOME_METABOLISM_OF_RNA |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: RBM8A |
MedGen: RBM8A (Human Medical Genetics with Condition) | |
ClinVar: RBM8A | |
Phenotype | MGI: RBM8A (International Mouse Phenotyping Consortium) |
PhenomicDB: RBM8A |
Mutations for RBM8A |
* 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 RBM8A 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 |
CR736380 | RBM8A | 1 | 74 | 1 | 145510185 | 145510258 | DYNLRB1 | 70 | 475 | 20 | 33114114 | 33128587 | |
DA211154 | RBM8A | 1 | 153 | 1 | 145507640 | 145508074 | SOS1 | 150 | 498 | 2 | 39212826 | 39213173 | |
AI962310 | FRMPD3 | 12 | 270 | X | 106848223 | 106848481 | RBM8A | 265 | 351 | 1 | 145507685 | 145507770 | |
AW590132 | FRMPD3 | 1 | 259 | X | 106848223 | 106848481 | RBM8A | 254 | 339 | 1 | 145507685 | 145507770 | |
BG999583 | ITSN2 | 19 | 464 | 2 | 24431760 | 24432803 | RBM8A | 456 | 477 | 1 | 145511736 | 145511757 |
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=17) | (# total SNVs=2) |
(# 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 |
chr1:145509207-145509207 | p.R174H | 2 |
chr1:145509007-145509007 | p.S145N | 2 |
chr1:145507706-145507706 | p.D14H | 1 |
chr1:145509040-145509040 | p.K156T | 1 |
chr1:145508024-145508024 | p.H26Y | 1 |
chr1:145509174-145509174 | p.R163Q | 1 |
chr1:145508226-145508226 | p.R49R | 1 |
chr1:145509177-145509177 | p.R164I | 1 |
chr1:145508250-145508250 | p.V57V | 1 |
chr1:145509197-145509197 | p.R171W | 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 |   | 2 |   | 2 |   |   |   |   | 2 |   |   | 1 | 2 |   |   |   |   | 1 |   | 2 |
# mutation |   | 2 |   | 2 |   |   |   |   | 2 |   |   | 1 | 2 |   |   |   |   | 1 |   | 2 |
nonsynonymous SNV |   | 2 |   | 2 |   |   |   |   | 2 |   |   | 1 | 2 |   |   |   |   | 1 |   | 2 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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 |
chr1:145509207 | p.R174H | 2 |
chr1:145509017 | p.D60H | 1 |
chr1:145509027 | p.G65V | 1 |
chr1:145509040 | p.I99L | 1 |
chr1:145509177 | p.W148C | 1 |
chr1:145509204 | p.R152W | 1 |
chr1:145507682 | p.K156T | 1 |
chr1:145507688 | p.R164I | 1 |
chr1:145508257 | p.R173L | 1 |
chr1:145508273 | p.D6N | 1 |
Other DBs for Point Mutations |
Copy Number for RBM8A 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 RBM8A |
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 |
ANP32E,APH1A,CHTOP,CHD1L,GATAD2B,GNRHR2,GPR89A, GPX6,ILF2,LIX1,MRPL9,PEX11B,PIPSL,POLR3C, PRUNE,RBM8A,RNF115,SCNM1,SETDB1,VPS72,ZNF286B | CBX1,CTBP2,DDX31,DKC1,DSP,ERBB3,ESRP1, FIP1L1,FUBP1,GRHL2,ISG20L2,KDM1A,LIG3,LUC7L2, MYO5B,NOLC1,PRPF4,PSPC1,RBM8A,SHROOM3,SPATS2 |
ANP32E,CHTOP,CDC73,COPA,FAM20B,GATAD2B,ILF2, IPO9,NME7,NUCKS1,PARP1,PRCC,RBBP5,RBM8A, SLC25A44,SNX27,UBAP2L,UBE2Q1,UBQLN4,VPS45,YY1AP1 | CCT5,CDC5L,CDC6,DONSON,FAM111B,FUBP1,HELLS, ISG20L2,KIAA0020,MCM10,MCM4,MSH2,NUPL1,RAD51, RBM17,RBM8A,RFC3,SRSF1,TIPIN,TRA2B,ZWILCH |
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 RBM8A |
There's no related Drug. |
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Cross referenced IDs for RBM8A |
* 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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