Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolSDHC
Gene namesuccinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa
SynonymsCYB560|CYBL|PGL3|QPS1|SDH3
CytomapUCSC genome browser: 1q23.3
Genomic locationchr1 :161284165-161334535
Type of geneprotein-coding
RefGenesNM_001035511.1,
NM_001035512.1,NM_001035513.1,NM_001278172.1,NM_003001.3,
NR_103459.1,
Ensembl idENSG00000143252
Descriptioncytochrome 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 date20141219
dbXrefs MIM : 602413
HGNC : HGNC
HPRD : 03878
ProteinUniProt: Q99643
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SDHC
BioGPS: 6391
Gene Expression Atlas: ENSG00000143252
The Human Protein Atlas: ENSG00000143252
PathwayNCI Pathway Interaction Database: SDHC
KEGG: SDHC
REACTOME: SDHC
ConsensusPathDB
Pathway Commons: SDHC
MetabolismMetaCyc: SDHC
HUMANCyc: SDHC
RegulationEnsembl's Regulation: ENSG00000143252
miRBase: chr1 :161,284,165-161,334,535
TargetScan: NM_001035511
cisRED: ENSG00000143252
ContextiHOP: SDHC
cancer metabolism search in PubMed: SDHC
UCL Cancer Institute: SDHC
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SDHC in cancer cell metabolism1. Baysal BE (2003) On the association of succinate dehydrogenase mutations with hereditary paraganglioma. Trends in Endocrinology & Metabolism 14: 453-459. go to article

Top
Phenotypic Information for SDHC(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

check002.gifOthers
OMIM 602413; gene.
605373; phenotype.
606864; phenotype.
Orphanet 201; Cowden syndrome.
29072; Hereditary pheochromocytoma-paraganglioma.
44890; Gastrointestinal stromal tumor.
97286; Carney-Stratakis syndrome.
DiseaseKEGG Disease: SDHC
MedGen: SDHC (Human Medical Genetics with Condition)
ClinVar: SDHC
PhenotypeMGI: SDHC (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovarySDHCchr1161309129161309149SDHCchr1161309589161309609
ovarySDHCchr1161314845161314865MTMR8chr236351570463515724
pancreasSDHCchr1161293775161293795chr137927159179271611
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SDHC related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample                2
GAIN (# sample)                2
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)

Top
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=1

Top
check002.gifSomatic 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.

Top
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
chr1:161326467-161326467p.G81E1
chr1:161284214-161284214p.R7R1
chr1:161326471-161326471p.V82V1
chr1:161293414-161293414p.R11C1
chr1:161326623-161326623p.R133Q1
chr1:161298183-161298183p.?1
chr1:161332149-161332149p.P146S1
chr1:161298193-161298193p.P29S1
chr1:161298208-161298208p.A34T1
chr1:161298242-161298242p.N45S1

Top
check002.gifSNV 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 ID1234567891011121314151617181920
# sample2  1       1 1  31 4
# mutation2  1       1 1  31 6
nonsynonymous SNV2          1 1  31 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])

Top
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
chr1:161326518p.K111K,SDHC1
chr1:161284214p.F112L,SDHC1
chr1:161326568p.S7R1
chr1:161293414p.R11C,SDHC1
chr1:161332149p.P29S,SDHC1
chr1:161298193p.A34T,SDHC1
chr1:161332256p.S48L,SDHC1
chr1:161298208p.P54T,SDHC1
chr1:161332312p.P11L,SDHC1
chr1:161298251p.A13V,SDHC1

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 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]

Top
Gene Expression for SDHC

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

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
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for SDHC
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA35607; -.
Organism-specific databasesCTD 6391; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00139succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDaapproved; nutraceuticalSuccinic acid
DB04141succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDaexperimental2-Hexyloxy-6-Hydroxymethyl-Tetrahydro-Pyran-3,4,5-Triol
DB08689succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDaexperimentalUBIQUINONE-1


Top
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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas