Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 SIN3B
Basic gene info.Gene symbolSIN3B
Gene nameSIN3 transcription regulator family member B
Synonyms-
CytomapUCSC genome browser: 19p13.11
Genomic locationchr19 :16940208-16991164
Type of geneprotein-coding
RefGenesNM_001297595.1,
NM_001297597.1,NM_015260.3,
Ensembl idENSG00000127511
DescriptionSIN3 homolog B, transcriptional regulatorSIN3 transcription regulator homolog Bhistone deacetylase complex subunit Sin3bpaired amphipathic helix protein Sin3btranscriptional corepressor Sin3b
Modification date20141207
dbXrefs MIM : 607777
HGNC : HGNC
Ensembl : ENSG00000127511
HPRD : 09691
Vega : OTTHUMG00000182642
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SIN3B
BioGPS: 23309
Gene Expression Atlas: ENSG00000127511
The Human Protein Atlas: ENSG00000127511
PathwayNCI Pathway Interaction Database: SIN3B
KEGG: SIN3B
REACTOME: SIN3B
ConsensusPathDB
Pathway Commons: SIN3B
MetabolismMetaCyc: SIN3B
HUMANCyc: SIN3B
RegulationEnsembl's Regulation: ENSG00000127511
miRBase: chr19 :16,940,208-16,991,164
TargetScan: NM_001297595
cisRED: ENSG00000127511
ContextiHOP: SIN3B
cancer metabolism search in PubMed: SIN3B
UCL Cancer Institute: SIN3B
Assigned class in ccmGDBC

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Phenotypic Information for SIN3B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SIN3B
Familial Cancer Database: SIN3B
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SIN3B
MedGen: SIN3B (Human Medical Genetics with Condition)
ClinVar: SIN3B
PhenotypeMGI: SIN3B (International Mouse Phenotyping Consortium)
PhenomicDB: SIN3B

Mutations for SIN3B
* 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

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastSIN3Bchr191696705316967053CPAMD8chr191707951217079512
ovarySIN3Bchr191697345516973475PRKACAchr191422175014221770
ovarySIN3Bchr191697468116974701KIAA0355chr193481096734810987
ovarySIN3Bchr191698048316980503chr1984709238470943
pancreasSIN3Bchr191696212616962146SIN3Bchr191698369316983713
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SIN3B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ308641SIN3B2232191698042016980652SIN3B227288191698029916980359
BQ181363YEATS2194363183529995183530411SIN3B433670191695446516954702
BF365213SIN3B14281191694499916945267SIN3B275327191694529516945347

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1      
GAIN (# sample)          1      
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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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=66)
Stat. for Synonymous SNVs
(# total SNVs=25)
Stat. for Deletions
(# total SNVs=4)
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
chr19:16973291-16973291p.R396H3
chr19:16973238-16973238p.S378S2
chr19:16987016-16987016p.M947V2
chr19:16957798-16957798p.T200T2
chr19:16973290-16973290p.R396C2
chr19:16976289-16976289p.S516S2
chr19:16952630-16952630p.P145S2
chr19:16942395-16942395p.L106L2
chr19:16974595-16974595p.D489D2
chr19:16965033-16965033p.S340Y2

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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
# sample14 14  5221 533  1312111
# mutation14 16  5221 533  1415115
nonsynonymous SNV 3 8  4121 133  511111
synonymous SNV11 8  11   4    94 4
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
chr19:16974595p.R396C,SIN3B2
chr19:16977262p.L106L,SIN3B2
chr19:16973290p.A157A,SIN3B2
chr19:16942395p.P145S,SIN3B2
chr19:16952630p.D47D,SIN3B2
chr19:16986967p.P248P,SIN3B1
chr19:16952673p.P78L,SIN3B1
chr19:16962311p.A311A,SIN3B1
chr19:16977229p.C249C,SIN3B1
chr19:16973243p.R396H,SIN3B1

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 SIN3B 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 SIN3B

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

AKAP8,ANO8,BRD4,C19orf44,CC2D1A,CCDC130,CHERP,
DCAF15,DDA1,ELL,GTPBP3,MAU2,MED26,MRI1,
MYO9B,RFX1,SIN3B,TSSK6,TYK2,WIZ,YJEFN3
ABCC10,ANKRD11,CEP164,CUL9,GIGYF1,MAU2,ZSWIM8,
LENG8,MAPK8IP3,MBD1,MINK1,MYO15B,NEURL4,NISCH,
PGS1,RTEL1,SIN3B,TAF1C,TUBGCP6,ZNF335,ZNF646

AKAP8L,BRD4,SOGA1,CCDC130,COLQ,CRTC1,CUL9,
DOCK6,ELL,MAU2,MLLT1,MYO9B,NISCH,PKD1,
PPP1R12C,SEMA6C,SIN3B,SYNGAP1,TYK2,WIZ,ZNF333
ASXL1,ATXN2,PRRC2B,CEP164,CHD6,CRAMP1L,GIGYF1,
INTS3,L3MBTL1,LZTR1,NISCH,OBSCN,PPT2,SETD5,
SFSWAP,SIN3B,SSH1,SYNGAP1,ZC3H7B,ZDHHC8,ZNF142
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 SIN3B


There's no related Drug.
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Cross referenced IDs for SIN3B
* 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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