Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for SNRPB
Basic gene info.Gene symbolSNRPB
Gene namesmall nuclear ribonucleoprotein polypeptides B and B1
SynonymsCOD|SNRPB1|Sm-B/B'|SmB/B'|SmB/SmB'|snRNP-B
CytomapUCSC genome browser: 20p13
Genomic locationchr20 :2442280-2451499
Type of geneprotein-coding
RefGenesNM_003091.3,
NM_198216.1,
Ensembl idENSG00000125835
DescriptionB 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 date20141207
dbXrefs MIM : 182282
HGNC : HGNC
Ensembl : ENSG00000125835
HPRD : 01655
Vega : OTTHUMG00000031694
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SNRPB
BioGPS: 6628
Gene Expression Atlas: ENSG00000125835
The Human Protein Atlas: ENSG00000125835
PathwayNCI Pathway Interaction Database: SNRPB
KEGG: SNRPB
REACTOME: SNRPB
ConsensusPathDB
Pathway Commons: SNRPB
MetabolismMetaCyc: SNRPB
HUMANCyc: SNRPB
RegulationEnsembl's Regulation: ENSG00000125835
miRBase: chr20 :2,442,280-2,451,499
TargetScan: NM_003091
cisRED: ENSG00000125835
ContextiHOP: SNRPB
cancer metabolism search in PubMed: SNRPB
UCL Cancer Institute: SNRPB
Assigned class in ccmGDBC

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Phenotypic Information for SNRPB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SNRPB
Familial Cancer Database: SNRPB
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_NON_CODING_RNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SNRPB
MedGen: SNRPB (Human Medical Genetics with Condition)
ClinVar: SNRPB
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SNRPB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE252218TCFL52158206147683061476986SNRPB1546162024444132451402
BG472482TCFL523179206147683061476986SNRPB1754402024464212451402
BG472537TCFL516179206147682361476986SNRPB1756542024443972451402
CB157749BOK1762242513231242513306SNRPB654512024445022451415
BF871894TMCC1122703129512972129513228SNRPB2613392024439982444076

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr20:2442418-2442418p.R236H4
chr20:2443348-2443348p.P207S2
chr20:2444418-2444418p.R132L2
chr20:2443759-2443759p.M179V2
chr20:2443294-2443294p.P225S1
chr20:2448288-2448288p.L40F1
chr20:2443865-2443865p.T143T1
chr20:2446385-2446385p.S79L1
chr20:2443347-2443347p.P207R1
chr20:2448314-2448314p.K32E1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  41 2 2  232  62 2
# mutation2  41 2 2  232  72 2
nonsynonymous SNV2  31 1 1  131  51 1
synonymous SNV   1  1 1  1 1  21 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr20:2442418p.R236H2
chr20:2443404p.R172H,SNRPB1
chr20:2446385p.H12R,SNRPB1
chr20:2443759p.A164S,SNRPB1
chr20:2446399p.S6S,SNRPB1
chr20:2443766p.T143T,SNRPB1
chr20:2446420p.V3V,SNRPB1
chr20:2443779p.V141V,SNRPB1
chr20:2446424p.P137T,SNRPB1
chr20:2443804p.R132L,SNRPB1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

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
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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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

: Open all cross reference information



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