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 SIN3A
Basic gene info.Gene symbolSIN3A
Gene nameSIN3 transcription regulator family member A
Synonyms-
CytomapUCSC genome browser: 15q24.2
Genomic locationchr15 :75661719-75743926
Type of geneprotein-coding
RefGenesNM_001145357.1,
NM_001145358.1,NM_015477.2,
Ensembl idENSG00000169375
DescriptionSIN3 homolog A, transcription regulatorSIN3 transcription regulator homolog Ahistone deacetylase complex subunit Sin3apaired amphipathic helix protein Sin3atranscriptional co-repressor Sin3Atranscriptional corepressor Sin3atranscriptional regulator,
Modification date20141207
dbXrefs MIM : 607776
HGNC : HGNC
Ensembl : ENSG00000169375
HPRD : 09690
Vega : OTTHUMG00000142834
ProteinUniProt: Q96ST3
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SIN3A
BioGPS: 25942
Gene Expression Atlas: ENSG00000169375
The Human Protein Atlas: ENSG00000169375
PathwayNCI Pathway Interaction Database: SIN3A
KEGG: SIN3A
REACTOME: SIN3A
ConsensusPathDB
Pathway Commons: SIN3A
MetabolismMetaCyc: SIN3A
HUMANCyc: SIN3A
RegulationEnsembl's Regulation: ENSG00000169375
miRBase: chr15 :75,661,719-75,743,926
TargetScan: NM_001145357
cisRED: ENSG00000169375
ContextiHOP: SIN3A
cancer metabolism search in PubMed: SIN3A
UCL Cancer Institute: SIN3A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for SIN3A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SIN3A
Familial Cancer Database: SIN3A
* 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 UCEC 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 607776; gene.
Orphanet
DiseaseKEGG Disease: SIN3A
MedGen: SIN3A (Human Medical Genetics with Condition)
ClinVar: SIN3A
PhenotypeMGI: SIN3A (International Mouse Phenotyping Consortium)
PhenomicDB: SIN3A

Mutations for SIN3A
* 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 SIN3A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI054950SIN3A17153157570515975705295SGCZ13915981491217114912191
AW851387SIN3A1466157567661575684714SIN3A463640157568712575688696
AW866901FIS1242707100885885100887158SIN3A267391157572265575743795
BQ346619SIN3A8104157568482975684925ZNF57797165195237664852376715
AW006026SIN3A194157566347575663568DHODH87623167204845072057095
BF366946SIN3A38146157568481675684925ZNF577139206195237664852376715
BF764786AFAP11260477915267791786SIN3A258347157566805775668146

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=130)
Stat. for Synonymous SNVs
(# total SNVs=33)
Stat. for Deletions
(# total SNVs=6)
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
chr15:75706642-75706642p.A126V4
chr15:75673043-75673043p.R1104*4
chr15:75684631-75684631p.R935*3
chr15:75694278-75694278p.E481K3
chr15:75705213-75705213p.I216T2
chr15:75684761-75684763p.N891delN2
chr15:75692404-75692404p.R611C2
chr15:75699483-75699483p.K440N2
chr15:75693132-75693132p.R559Q2
chr15:75694205-75694205p.S505C2

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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
# sample332203 5 22 433  1412 19
# mutation332303 5 22 533  1513 25
nonsynonymous SNV332233 2 1  432  1111 20
synonymous SNV   7  3 12 1 1  42 5
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
chr15:75684776p.Q422R,SIN3A2
chr15:75702229p.F886F,SIN3A2
chr15:75706642p.A126V,SIN3A2
chr15:75692404p.R611G,SIN3A2
chr15:75702524p.S587S,SIN3A1
chr15:75674045p.I216T,SIN3A1
chr15:75688742p.K1164K,SIN3A1
chr15:75705247p.R19Q,SIN3A1
chr15:75684663p.I933V,SIN3A1
chr15:75693090p.E752V,SIN3A1

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 SIN3A 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 SIN3A

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

AAGAB,ARIH1,BBS4,CLPX,CSNK1G1,DENND4A,DIS3L,
DPP8,FEM1B,HMG20A,IREB2,MYO9A,NEO1,PIAS1,
PTPN9,RNF111,SCAPER,SIN3A,SLC24A1,VPS13C,ZNF609
ADNP,ARHGAP32,CBFA2T2,CHD2,CHD6,CHD8,CTNND1,
DSG2,GTF3C4,RCAN3,SIN3A,SPEF2,SUV420H1,ZNF12,
ZNF134,ZNF229,ZNF268,ZNF33A,ZNF430,ZNF594,ZZZ3

ADAM10,ARIH1,CSNK1G1,DENND4A,DPP8,EDC3,FAM98B,
FEM1B,HERC1,INO80,IREB2,PIAS1,PTPN9,RFX7,
RNF111,RTF1,SIN3A,SNX1,ZNF106,ZNF592,ZNF609
ACVR2B,ADNP,ATF7IP,BCOR,CBL,GATAD2B,GLG1,
KDM3B,GLTSCR1L,KIAA1429,LSM14B,KAT7,NUMA1,RNF20,
RPRD2,SIN3A,SMARCA2,SUFU,UBE4B,UBR5,ZMYM3
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 SIN3A


There's no related Drug.
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Cross referenced IDs for SIN3A
* 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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