Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	SIN3A
	Gene name	SIN3 transcription regulator family member A
	Synonyms	-
	Cytomap	UCSC genome browser: 15q24.2
	Genomic location	chr15 :75661719-75743926
	Type of gene	protein-coding
	RefGenes	NM_001145357.1, NM_001145358.1,NM_015477.2,
	Ensembl id	ENSG00000169375
	Description	SIN3 homolog A, transcription regulatorSIN3 transcription regulator homolog Ahistone deacetylase complex subunit Sin3apaired amphipathic helix protein Sin3atranscriptional co-repressor Sin3Atranscriptional corepressor Sin3atranscriptional regulator,
	Modification date	20141207
dbXrefs	MIM : 607776
	HGNC : HGNC
	Ensembl : ENSG00000169375
	HPRD : 09690
	Vega : OTTHUMG00000142834
Protein	UniProt: Q96ST3 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SIN3A
	BioGPS: 25942
	Gene Expression Atlas: ENSG00000169375
	The Human Protein Atlas: ENSG00000169375
Pathway	NCI Pathway Interaction Database: SIN3A
	KEGG: SIN3A
	REACTOME: SIN3A
	ConsensusPathDB
	Pathway Commons: SIN3A
Metabolism	MetaCyc: SIN3A
	HUMANCyc: SIN3A
Regulation	Ensembl's Regulation: ENSG00000169375
	miRBase: chr15 :75,661,719-75,743,926
	TargetScan: NM_001145357
	cisRED: ENSG00000169375
Context	iHOP: SIN3A
	cancer metabolism search in PubMed: SIN3A
	UCL Cancer Institute: SIN3A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for SIN3A(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	607776; gene.
Orphanet
Disease	KEGG Disease: SIN3A
	MedGen: SIN3A (Human Medical Genetics with Condition)
	ClinVar: SIN3A
Phenotype	MGI: SIN3A (International Mouse Phenotyping Consortium)
Phenotype	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.

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 SIN3A 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
BI054950	SIN3A	17	153	15	75705159	75705295	SGCZ	139	159	8	14912171	14912191
AW851387	SIN3A	1	466	15	75676615	75684714	SIN3A	463	640	15	75687125	75688696
AW866901	FIS1	24	270	7	100885885	100887158	SIN3A	267	391	15	75722655	75743795
BQ346619	SIN3A	8	104	15	75684829	75684925	ZNF577	97	165	19	52376648	52376715
AW006026	SIN3A	1	94	15	75663475	75663568	DHODH	87	623	16	72048450	72057095
BF366946	SIN3A	38	146	15	75684816	75684925	ZNF577	139	206	19	52376648	52376715
BF764786	AFAP1	1	260	4	7791526	7791786	SIN3A	258	347	15	75668057	75668146

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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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
chr15:75706642-75706642	p.A126V	4
chr15:75673043-75673043	p.R1104*	4
chr15:75694278-75694278	p.E481K	3
chr15:75684631-75684631	p.R935*	3
chr15:75702228-75702228	p.Q422Q	2
chr15:75687179-75687179	p.R707*	2
chr15:75693184-75693184	p.I542L	2
chr15:75702229-75702229	p.Q422R	2
chr15:75694308-75694308	p.R471*	2
chr15:75702279-75702279	p.G405G	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	3	3	2	20	3		5		2	2		4	3	3			14	12		19
# mutation	3	3	2	30	3		5		2	2		5	3	3			15	13		25
nonsynonymous SNV	3	3	2	23	3		2		1			4	3	2			11	11		20
synonymous SNV				7			3		1	2		1		1			4	2		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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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
chr15:75702229	p.F886F,SIN3A	2
chr15:75706642	p.A126V,SIN3A	2
chr15:75692404	p.R611G,SIN3A	2
chr15:75684776	p.Q422R,SIN3A	2
chr15:75687043	p.I150I,SIN3A	1
chr15:75722661	p.E1080K,SIN3A	1
chr15:75668105	p.V692V,SIN3A	1
chr15:75682045	p.D547Y,SIN3A	1
chr15:75692389	p.L372V,SIN3A	1
chr15:75703963	p.L1234R,SIN3A	1

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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