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 SIN3B

Basic gene info.	Gene symbol	SIN3B
	Gene name	SIN3 transcription regulator family member B
	Synonyms	-
	Cytomap	UCSC genome browser: 19p13.11
	Genomic location	chr19 :16940208-16991164
	Type of gene	protein-coding
	RefGenes	NM_001297595.1, NM_001297597.1,NM_015260.3,
	Ensembl id	ENSG00000127511
	Description	SIN3 homolog B, transcriptional regulatorSIN3 transcription regulator homolog Bhistone deacetylase complex subunit Sin3bpaired amphipathic helix protein Sin3btranscriptional corepressor Sin3b
	Modification date	20141207
dbXrefs	MIM : 607777
	HGNC : HGNC
	Ensembl : ENSG00000127511
	HPRD : 09691
	Vega : OTTHUMG00000182642
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SIN3B
	BioGPS: 23309
	Gene Expression Atlas: ENSG00000127511
	The Human Protein Atlas: ENSG00000127511
Pathway	NCI Pathway Interaction Database: SIN3B
	KEGG: SIN3B
	REACTOME: SIN3B
	ConsensusPathDB
	Pathway Commons: SIN3B
Metabolism	MetaCyc: SIN3B
	HUMANCyc: SIN3B
Regulation	Ensembl's Regulation: ENSG00000127511
	miRBase: chr19 :16,940,208-16,991,164
	TargetScan: NM_001297595
	cisRED: ENSG00000127511
Context	iHOP: SIN3B
	cancer metabolism search in PubMed: SIN3B
	UCL Cancer Institute: SIN3B
Assigned class in ccmGDB	C

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Phenotypic Information for SIN3B(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: SIN3B
	MedGen: SIN3B (Human Medical Genetics with Condition)
	ClinVar: SIN3B
Phenotype	MGI: SIN3B (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	SIN3B	chr19	16967053	16967053	CPAMD8	chr19	17079512	17079512
ovary	SIN3B	chr19	16973455	16973475	PRKACA	chr19	14221750	14221770
ovary	SIN3B	chr19	16974681	16974701	KIAA0355	chr19	34810967	34810987
ovary	SIN3B	chr19	16980483	16980503		chr19	8470923	8470943
pancreas	SIN3B	chr19	16962126	16962146	SIN3B	chr19	16983693	16983713

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SIN3B 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
BQ308641	SIN3B	2	232	19	16980420	16980652	SIN3B	227	288	19	16980299	16980359
BQ181363	YEATS2	19	436	3	183529995	183530411	SIN3B	433	670	19	16954465	16954702
BF365213	SIN3B	14	281	19	16944999	16945267	SIN3B	275	327	19	16945295	16945347

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=5

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Somatic 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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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
chr19:16973291-16973291	p.R396H	3
chr19:16973290-16973290	p.R396C	2
chr19:16976289-16976289	p.S516S	2
chr19:16952630-16952630	p.P145S	2
chr19:16942395-16942395	p.L106L	2
chr19:16974595-16974595	p.D489D	2
chr19:16965033-16965033	p.S340Y	2
chr19:16989099-16989099	p.C1052C	2
chr19:16940697-16940697	p.F72L	2
chr19:16989521-16989521	p.R1158C	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	1	4		14			5	2	2	1		5	3	3			13	12	1	11
# mutation	1	4		16			5	2	2	1		5	3	3			14	15	1	15
nonsynonymous SNV		3		8			4	1	2	1		1	3	3			5	11	1	11
synonymous SNV	1	1		8			1	1				4					9	4		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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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
chr19:16952630	p.A157A,SIN3B	2
chr19:16974595	p.P145S,SIN3B	2
chr19:16977262	p.D47D,SIN3B	2
chr19:16942395	p.L106L,SIN3B	2
chr19:16973290	p.R396C,SIN3B	2
chr19:16942408	p.T424T,SIN3B	1
chr19:16973291	p.Q127H,SIN3B	1
chr19:16980673	p.P277L,SIN3B	1
chr19:16957837	p.P22L,SIN3B	1
chr19:16976225	p.F442C,SIN3B	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 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

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


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

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 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