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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SNRPB |
Basic gene info. | Gene symbol | SNRPB |
Gene name | small nuclear ribonucleoprotein polypeptides B and B1 | |
Synonyms | COD|SNRPB1|Sm-B/B'|SmB/B'|SmB/SmB'|snRNP-B | |
Cytomap | UCSC genome browser: 20p13 | |
Genomic location | chr20 :2442280-2451499 | |
Type of gene | protein-coding | |
RefGenes | NM_003091.3, NM_198216.1, | |
Ensembl id | ENSG00000125835 | |
Description | B polypeptide of Sm proteinSm protein B/B'sm-B/Sm-B'small nuclear ribonucleoprotein polypeptide Bsmall nuclear ribonucleoprotein polypeptides B and B'small nuclear ribonucleoprotein-associated proteins B and B' | |
Modification date | 20141207 | |
dbXrefs | MIM : 182282 | |
HGNC : HGNC | ||
Ensembl : ENSG00000125835 | ||
HPRD : 01655 | ||
Vega : OTTHUMG00000031694 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SNRPB | |
BioGPS: 6628 | ||
Gene Expression Atlas: ENSG00000125835 | ||
The Human Protein Atlas: ENSG00000125835 | ||
Pathway | NCI Pathway Interaction Database: SNRPB | |
KEGG: SNRPB | ||
REACTOME: SNRPB | ||
ConsensusPathDB | ||
Pathway Commons: SNRPB | ||
Metabolism | MetaCyc: SNRPB | |
HUMANCyc: SNRPB | ||
Regulation | Ensembl's Regulation: ENSG00000125835 | |
miRBase: chr20 :2,442,280-2,451,499 | ||
TargetScan: NM_003091 | ||
cisRED: ENSG00000125835 | ||
Context | iHOP: SNRPB | |
cancer metabolism search in PubMed: SNRPB | ||
UCL Cancer Institute: SNRPB | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for SNRPB(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SNRPB |
Familial Cancer Database: SNRPB |
* 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_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: SNRPB |
MedGen: SNRPB (Human Medical Genetics with Condition) | |
ClinVar: SNRPB | |
Phenotype | MGI: SNRPB (International Mouse Phenotyping Consortium) |
PhenomicDB: SNRPB |
Mutations for SNRPB |
* 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 SNRPB 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 |
BE252218 | TCFL5 | 2 | 158 | 20 | 61476830 | 61476986 | SNRPB | 154 | 616 | 20 | 2444413 | 2451402 | |
BG472482 | TCFL5 | 23 | 179 | 20 | 61476830 | 61476986 | SNRPB | 175 | 440 | 20 | 2446421 | 2451402 | |
BG472537 | TCFL5 | 16 | 179 | 20 | 61476823 | 61476986 | SNRPB | 175 | 654 | 20 | 2444397 | 2451402 | |
CB157749 | BOK | 1 | 76 | 2 | 242513231 | 242513306 | SNRPB | 65 | 451 | 20 | 2444502 | 2451415 | |
BF871894 | TMCC1 | 12 | 270 | 3 | 129512972 | 129513228 | SNRPB | 261 | 339 | 20 | 2443998 | 2444076 |
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=24) | (# total SNVs=7) |
(# 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 |
chr20:2442418-2442418 | p.R236H | 4 |
chr20:2443348-2443348 | p.P207S | 2 |
chr20:2444418-2444418 | p.R132L | 2 |
chr20:2443759-2443759 | p.M179V | 2 |
chr20:2444404-2444404 | p.P137T | 1 |
chr20:2446387-2446387 | p.V78V | 1 |
chr20:2448333-2448333 | p.R25R | 1 |
chr20:2446398-2446398 | p.E75K | 1 |
chr20:2448373-2448373 | p.H12R | 1 |
chr20:2443366-2443366 | p.P201S | 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 |   |   | 4 | 1 |   | 2 |   | 2 |   |   | 2 | 3 | 2 |   |   | 6 | 2 |   | 2 |
# mutation | 2 |   |   | 4 | 1 |   | 2 |   | 2 |   |   | 2 | 3 | 2 |   |   | 7 | 2 |   | 2 |
nonsynonymous SNV | 2 |   |   | 3 | 1 |   | 1 |   | 1 |   |   | 1 | 3 | 1 |   |   | 5 | 1 |   | 1 |
synonymous SNV |   |   |   | 1 |   |   | 1 |   | 1 |   |   | 1 |   | 1 |   |   | 2 | 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 |
chr20:2442418 | p.R236H | 2 |
chr20:2446399 | p.V3V,SNRPB | 1 |
chr20:2443766 | p.T143T,SNRPB | 1 |
chr20:2446420 | p.V141V,SNRPB | 1 |
chr20:2443779 | p.P137T,SNRPB | 1 |
chr20:2446424 | p.R132L,SNRPB | 1 |
chr20:2443804 | p.A110P,SNRPB | 1 |
chr20:2446432 | p.E83D,SNRPB | 1 |
chr20:2443865 | p.P233S | 1 |
chr20:2448273 | p.S79L,SNRPB | 1 |
Other DBs for Point Mutations |
Copy Number for SNRPB 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 SNRPB |
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 |
BAX,C1orf35,C20orf27,CCDC124,CDC34,CENPB,FAM96B, IDH3B,ITPA,LSM4,LSM7,MRPL55,MRPS26,MXD3, NDUFA11,NOC4L,NOP56,RALY,RPP21,SNRPB,PAM16 | BCL2L12,ACTL10,CHCHD6,DCTPP1,EIF6,EXOSC4,HSPBP1, JMJD4,LSM7,LYPLA2,NHP2,NOC4L,OTUB1,PAFAH1B3, PUF60,PYCRL,SNRPB,STMN3,THOC6,TRAPPC6A,YIPF2 |
C20orf196,C20orf27,AP5S1,TMEM230,NDUFAF5,CRLS1,DDRGK1, IDH3B,ITPA,LINC00493,MKKS,MRPS26,NAA20,NOP56, PANK2,PCNA,PSMF1,SNRPB2,SNRPB,TASP1,TRMT6 | BOLA3,HYPK,C1QBP,CDC123,DTYMK,EBNA1BP2,EMG1, MRPL52,MRTO4,NHP2,NME2,NPM3,NUP37,PFDN6, POP5,PPIH,RAN,SF3B5,SNRPB,STOML2,STRA13 |
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 SNRPB |
There's no related Drug. |
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Cross referenced IDs for SNRPB |
* 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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