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 SDHC

Basic gene info.	Gene symbol	SDHC
	Gene name	succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa
	Synonyms	CYB560\|CYBL\|PGL3\|QPS1\|SDH3
	Cytomap	UCSC genome browser: 1q23.3
	Genomic location	chr1 :161284165-161334535
	Type of gene	protein-coding
	RefGenes	NM_001035511.1, NM_001035512.1,NM_001035513.1,NM_001278172.1,NM_003001.3, NR_103459.1,
	Ensembl id	ENSG00000143252
	Description	cytochrome B large subunit of complex IIintegral membrane protein CII-3bsuccinate dehydrgenase cytochrome bsuccinate dehydrogenase 3, integral membrane subunitsuccinate dehydrogenase complex, subunit C, integral membrane protein, 15kDsuccinate dehydr
	Modification date	20141219
dbXrefs	MIM : 602413
	HGNC : HGNC
	HPRD : 03878
Protein	UniProt: Q99643 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SDHC
	BioGPS: 6391
	Gene Expression Atlas: ENSG00000143252
	The Human Protein Atlas: ENSG00000143252
Pathway	NCI Pathway Interaction Database: SDHC
	KEGG: SDHC
	REACTOME: SDHC
	ConsensusPathDB
	Pathway Commons: SDHC
Metabolism	MetaCyc: SDHC
	HUMANCyc: SDHC
Regulation	Ensembl's Regulation: ENSG00000143252
	miRBase: chr1 :161,284,165-161,334,535
	TargetScan: NM_001035511
	cisRED: ENSG00000143252
Context	iHOP: SDHC
	cancer metabolism search in PubMed: SDHC
	UCL Cancer Institute: SDHC
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SDHC 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

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

Cancer Description
Cancer	CGAP: SDHC
	Familial Cancer Database: SDHC

* 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	602413; gene. 605373; phenotype. 606864; phenotype.
Orphanet	201; Cowden syndrome. 29072; Hereditary pheochromocytoma-paraganglioma. 44890; Gastrointestinal stromal tumor. 97286; Carney-Stratakis syndrome.
Disease	KEGG Disease: SDHC
	MedGen: SDHC (Human Medical Genetics with Condition)
	ClinVar: SDHC
Phenotype	MGI: SDHC (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SDHC

Mutations for SDHC

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
ovary	SDHC	chr1	161309129	161309149	SDHC	chr1	161309589	161309609
ovary	SDHC	chr1	161314845	161314865	MTMR8	chr23	63515704	63515724
pancreas	SDHC	chr1	161293775	161293795		chr13	79271591	79271611

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 SDHC related fusion information.

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

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=1

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=4)	Stat. for Synonymous SNVs (# total SNVs=2)

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
chr1:161293414-161293414	p.R11C	1
chr1:161326623-161326623	p.R133Q	1
chr1:161298183-161298183	p.?	1
chr1:161332149-161332149	p.P146S	1
chr1:161298193-161298193	p.P29S	1
chr1:161298208-161298208	p.A34T	1
chr1:161298242-161298242	p.N45S	1
chr1:161298251-161298251	p.S48L	1
chr1:161298268-161298268	p.P54T	1
chr1:161310395-161310395	p.P64L	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=1

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	2			1								1		1			3	1		4
# mutation	2			1								1		1			3	1		6
nonsynonymous SNV	2											1		1			3	1		4
synonymous SNV				1																2

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
chr1:161293414	p.P29S,SDHC	1
chr1:161332149	p.A34T,SDHC	1
chr1:161298193	p.S48L,SDHC	1
chr1:161332256	p.P54T,SDHC	1
chr1:161298208	p.P11L,SDHC	1
chr1:161332312	p.A13V,SDHC	1
chr1:161298251	p.V29V,SDHC	1
chr1:161332315	p.S35S,SDHC	1
chr1:161298268	p.S45C,SDHC	1
chr1:161310395	p.T62A,SDHC	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 SDHC 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 SDHC

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


ATF6,B4GALT3,C1orf43,COPA,DAP3,DEDD,F11R, GBA,HAX1,NCSTN,NDUFS2,NIT1,PIGM,PYGO2, SLC50A1,SCAMP3,SDHC,SLC25A44,TOMM40L,UFC1,USP21	ACAT1,ATP5G3,ATPAF1,DLD,ETFA,ETFDH,FH, GHITM,GNPAT,HOXA10,HSDL2,HSPB6,ISCA1P1,PGM1, PHYH,PRDX3,SDHC,SETD3,SUCLA2,SUCLG2,WSB2

APH1A,ARPC5,BPNT1,C1orf43,DAP3,FH,FLAD1, HAX1,ILF2,MRPS14,NDUFS2,PEX19,SDHC,SNAPIN, TADA1,TFB2M,TIMM17A,TIPRL,TMEM183A,TPM3,TSNAX	AK2,ATP5C1,ATP5F1,ATP5H,C14orf2,COX16,HPRT1, MRPL13,MRPL16,MRPL39,MRPS22,MRPS28,MRPS35,MYCBP, NDUFA12,NDUFAB1,PPIA,PTGES3,SDHC,UQCRH,YWHAE

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 SDHC

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA35607; -.
Organism-specific databases	CTD	6391; -.

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 C, integral membrane protein, 15kDa	approved; nutraceutical	Succinic acid
DB04141	succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa	experimental	2-Hexyloxy-6-Hydroxymethyl-Tetrahydro-Pyran-3,4,5-Triol
DB08689	succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa	experimental	UBIQUINONE-1

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Cross referenced IDs for SDHC

* 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