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 SDHB

Basic gene info.	Gene symbol	SDHB
	Gene name	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)
	Synonyms	CWS2\|IP\|PGL4\|SDH\|SDH1\|SDH2\|SDHIP
	Cytomap	UCSC genome browser: 1p36.1-p35
	Genomic location	chr1 :17345224-17380665
	Type of gene	protein-coding
	RefGenes	NM_003000.2,
	Ensembl id	ENSG00000117118
	Description	iron-sulfur subunit of complex IIsuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
	Modification date	20141222
dbXrefs	MIM : 185470
	HGNC : HGNC
	Ensembl : ENSG00000117118
	HPRD : 01707
	Vega : OTTHUMG00000002289
Protein	UniProt: P21912 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SDHB
	BioGPS: 6390
	Gene Expression Atlas: ENSG00000117118
	The Human Protein Atlas: ENSG00000117118
Pathway	NCI Pathway Interaction Database: SDHB
	KEGG: SDHB
	REACTOME: SDHB
	ConsensusPathDB
	Pathway Commons: SDHB
Metabolism	MetaCyc: SDHB
	HUMANCyc: SDHB
Regulation	Ensembl's Regulation: ENSG00000117118
	miRBase: chr1 :17,345,224-17,380,665
	TargetScan: NM_003000
	cisRED: ENSG00000117118
Context	iHOP: SDHB
	cancer metabolism search in PubMed: SDHB
	UCL Cancer Institute: SDHB
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SDHB in cancer cell metabolism	1. Baysal BE (2003) On the association of succinate dehydrogenase mutations with hereditary paraganglioma. Trends in Endocrinology & Metabolism 14: 453-459. go to article 2. Aspuria P-JP, Lunt SY, Väremo L, Vergnes L, Gozo M, et al. (2014) Succinate dehydrogenase inhibition leads to epithelial-mesenchymal transition and reprogrammed carbon metabolism. Cancer & metabolism 2: 21. go to article

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

Cancer Description
Cancer	CGAP: SDHB
	Familial Cancer Database: SDHB

* 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_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

Others
OMIM	115310; phenotype. 171300; phenotype. 185470; gene. 606864; phenotype. 612359; phenotype.
Orphanet	201; Cowden syndrome. 29072; Hereditary pheochromocytoma-paraganglioma. 3208; Isolated succinate-CoQ reductase deficiency. 44890; Gastrointestinal stromal tumor. 97286; Carney-Stratakis syndrome.
Disease	KEGG Disease: SDHB
	MedGen: SDHB (Human Medical Genetics with Condition)
	ClinVar: SDHB
Phenotype	MGI: SDHB (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SDHB

Mutations for SDHB

* 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 SDHB 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
CB157553	SDHB	1	165	1	17371028	17380473	SDHB	159	622	1	17349203	17359639
BU608192	SDHB	2	303	1	17345217	17349187	SDHB	300	422	1	17349199	17350563
CB240554	SDHB	2	303	1	17345217	17349187	SDHB	300	422	1	17349199	17350563
N70468	SDHB	1	165	1	17345249	17345412	SDHB	160	372	1	17355181	17371329
BF840536	FOXK1	23	78	7	4809455	4809510	SDHB	70	314	1	17354572	17354815

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=17)	Stat. for Synonymous SNVs (# total SNVs=4)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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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
chr1:17349180-17349180	p.R230C	3
chr1:17355224-17355224	p.C98C	2
chr1:17345407-17345407	p.A271V	1
chr1:17345426-17345426	p.E265Q	1
chr1:17359560-17359560	p.R94T	1
chr1:17359563-17359563	p.C93Y	1
chr1:17350478-17350478	p.V211A	1
chr1:17371269-17371269	p.V63I	1
chr1:17350484-17350484	p.P209H	1
chr1:17371320-17371320	p.R46*	1

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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	1	2					1			2	2				1	5		2
# mutation		1	1	2					1			2	2				1	5		2
nonsynonymous SNV		1	1	2					1			1	1				1	4		2
synonymous SNV												1	1					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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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
chr1:17349180	p.R230C	2
chr1:17345426	p.K255R	1
chr1:17371269	p.V211A	1
chr1:17349104	p.P209H	1
chr1:17371343	p.G208E	1
chr1:17371358	p.S163Y	1
chr1:17350478	p.D161G	1
chr1:17380511	p.Q149Q	1
chr1:17350484	p.N106S	1
chr1:17350487	p.R94T	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 SDHB 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 SDHB

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


ATP5O,PITHD1,AUNIP,SZRD1,MINOS1,COX5A,COX7B, DDOST,EIF3I,LYPLA2,MRPL20,MRTO4,NUDC,PARK7, PGD,PSMA5,PSMB2,SDHB,SSU72,TRAPPC3,ZBTB8OS	ACAT1,ACO2,ALPK3,ATP5B,ADCK3,CHCHD10,CHCHD3, COX5A,MTFR1L,FH,HADHB,IMMT,MLYCD,NDUFA4, NDUFA9,PDHB,PHYH,SDHB,UQCRC2,UQCRFS1,VDAC2

AK2,ATP5C1,ATP5F1,ATP5G3,ATPIF1,MINOS1,C1QBP, COX8A,ECHS1,EIF3I,GOT1,MRPL37,MRTO4,PGD, PPP1R8,PSMA5,SDHB,SDHD,TMX2,UQCRC1,UQCRH	ATP5C1,ATP5F1,ATP5G3,ATPIF1,MPC1,C14orf2,C2orf47, COX6A1,ETFA,HINT1,MRPL48,MRPS36,NDUFB9,NDUFS3, PPA2,SDHB,SDHD,SUCLG1,UQCR10,UQCRC2,UQCRFS1

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 SDHB

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA35606; -.
Organism-specific databases	CTD	6390; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00139	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	approved; nutraceutical	Succinic acid
DB04141	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	experimental	2-Hexyloxy-6-Hydroxymethyl-Tetrahydro-Pyran-3,4,5-Triol
DB08689	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	experimental	UBIQUINONE-1

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Cross referenced IDs for SDHB

* 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