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 symbolSDHB
Gene namesuccinate dehydrogenase complex, subunit B, iron sulfur (Ip)
SynonymsCWS2|IP|PGL4|SDH|SDH1|SDH2|SDHIP
CytomapUCSC genome browser: 1p36.1-p35
Genomic locationchr1 :17345224-17380665
Type of geneprotein-coding
RefGenesNM_003000.2,
Ensembl idENSG00000117118
Descriptioniron-sulfur subunit of complex IIsuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
Modification date20141222
dbXrefs MIM : 185470
HGNC : HGNC
Ensembl : ENSG00000117118
HPRD : 01707
Vega : OTTHUMG00000002289
ProteinUniProt: P21912
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SDHB
BioGPS: 6390
Gene Expression Atlas: ENSG00000117118
The Human Protein Atlas: ENSG00000117118
PathwayNCI Pathway Interaction Database: SDHB
KEGG: SDHB
REACTOME: SDHB
ConsensusPathDB
Pathway Commons: SDHB
MetabolismMetaCyc: SDHB
HUMANCyc: SDHB
RegulationEnsembl's Regulation: ENSG00000117118
miRBase: chr1 :17,345,224-17,380,665
TargetScan: NM_003000
cisRED: ENSG00000117118
ContextiHOP: SDHB
cancer metabolism search in PubMed: SDHB
UCL Cancer Institute: SDHB
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SDHB 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
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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

check002.gifOthers
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.
DiseaseKEGG Disease: SDHB
MedGen: SDHB (Human Medical Genetics with Condition)
ClinVar: SDHB
PhenotypeMGI: SDHB (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SDHB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CB157553SDHB116511737102817380473SDHB15962211734920317359639
BU608192SDHB230311734521717349187SDHB30042211734919917350563
CB240554SDHB230311734521717349187SDHB30042211734919917350563
N70468SDHB116511734524917345412SDHB16037211735518117371329
BF840536FOXK12378748094554809510SDHB7031411735457217354815

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

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample   1      1      
GAIN (# sample)   1      1      
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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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=3

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check002.gifSomatic 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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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
chr1:17349180-17349180p.R230C3
chr1:17355224-17355224p.C98C2
chr1:17345426-17345426p.E265Q1
chr1:17359560-17359560p.R94T1
chr1:17359563-17359563p.C93Y1
chr1:17350478-17350478p.V211A1
chr1:17371269-17371269p.V63I1
chr1:17350484-17350484p.P209H1
chr1:17371320-17371320p.R46*1
chr1:17350517-17350517p.S198N1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample 112    1  22   15 2
# mutation 112    1  22   15 2
nonsynonymous SNV 112    1  11   14 2
synonymous SNV           11    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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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
chr1:17349180p.R230C2
chr1:17371269p.E265Q1
chr1:17349104p.K255R1
chr1:17371343p.V211A1
chr1:17371358p.P209H1
chr1:17350478p.G208E1
chr1:17380511p.S163Y1
chr1:17350484p.D161G1
chr1:17350487p.Q149Q1
chr1:17354296p.N106S1

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 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

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))
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check002.gifCNV 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
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

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
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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA35606; -.
Organism-specific databasesCTD 6390; -.

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 B, iron sulfur (Ip)approved; nutraceuticalSuccinic acid
DB04141succinate dehydrogenase complex, subunit B, iron sulfur (Ip)experimental2-Hexyloxy-6-Hydroxymethyl-Tetrahydro-Pyran-3,4,5-Triol
DB08689succinate dehydrogenase complex, subunit B, iron sulfur (Ip)experimentalUBIQUINONE-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



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