Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 SUCLG1
Basic gene info.Gene symbolSUCLG1
Gene namesuccinate-CoA ligase, alpha subunit
SynonymsGALPHA|MTDPS9|SUCLA1
CytomapUCSC genome browser: 2p11.2
Genomic locationchr2 :84650646-84686586
Type of geneprotein-coding
RefGenesNM_003849.3,
Ensembl idENSG00000163541
DescriptionSCS-alphasuccinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrialsuccinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrialsuccinyl-CoA synthetase subunit alpha
Modification date20141207
dbXrefs MIM : 611224
HGNC : HGNC
Ensembl : ENSG00000163541
HPRD : 18128
Vega : OTTHUMG00000130023
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SUCLG1
BioGPS: 8802
Gene Expression Atlas: ENSG00000163541
The Human Protein Atlas: ENSG00000163541
PathwayNCI Pathway Interaction Database: SUCLG1
KEGG: SUCLG1
REACTOME: SUCLG1
ConsensusPathDB
Pathway Commons: SUCLG1
MetabolismMetaCyc: SUCLG1
HUMANCyc: SUCLG1
RegulationEnsembl's Regulation: ENSG00000163541
miRBase: chr2 :84,650,646-84,686,586
TargetScan: NM_003849
cisRED: ENSG00000163541
ContextiHOP: SUCLG1
cancer metabolism search in PubMed: SUCLG1
UCL Cancer Institute: SUCLG1
Assigned class in ccmGDBC

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Phenotypic Information for SUCLG1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SUCLG1
Familial Cancer Database: SUCLG1
* 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
KEGG_PROPANOATE_METABOLISM
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SUCLG1
MedGen: SUCLG1 (Human Medical Genetics with Condition)
ClinVar: SUCLG1
PhenotypeMGI: SUCLG1 (International Mouse Phenotyping Consortium)
PhenomicDB: SUCLG1

Mutations for SUCLG1
* 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 SUCLG1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP319935SP10022652231280936231307732SUCLG125833928465065284650733
BM968054SUCLG1517028465085784652664SUCLG116742028465864084668196
BU607293SUCLG1517028465085784652664SUCLG116742028465864084668196

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 # sample1                
GAIN (# sample)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=24)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=2)

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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
chr2:84658736-84658736p.E241K4
chr2:84652606-84652606p.S316F3
chr2:84676841-84676841p.A45T2
chr2:84652539-84652539p.K338K2
chr2:84658722-84658722p.N245N1
chr2:84668443-84668443p.V153V1
chr2:84676772-84676772p.?1
chr2:84652628-84652628p.G309C1
chr2:84668507-84668507p.A132D1
chr2:84676817-84676817p.D53N1

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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
# sample1  32   6  4 1  25 3
# mutation1  32   6  4 1  25 3
nonsynonymous SNV1  12   4  2    22 2
synonymous SNV   2    2  2 1   3 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
chr2:84652703p.D246N1
chr2:84668483p.R47Q1
chr2:84686349p.A45T1
chr2:84658638p.N245N1
chr2:84668507p.S18R1
chr2:84658704p.E241K1
chr2:84668521p.V15V1
chr2:84658721p.Q220Q1
chr2:84668527p.T214T1
chr2:84658722p.G179V1

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 SUCLG1 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 SUCLG1

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

ATP5G3,ATP5O,BOLA3,PRADC1,CCT4,CCT7,COMMD1,
COX5A,COX7B,DGUOK,IMMT,KCMF1,MDH1,MDH2,
MRPS5,NDUFB3,RNF181,SF3B14,SNRPG,SUCLG1,VAMP8
APIP,BNIP3,CS,DECR1,DLST,GBE1,GPI,
HADH,MLX,MARC2,MRPS15,NDUFB5,NFU1,PDHA1,
PFKFB1,PPP1R1A,PRDX6,RNF157,STBD1,SUCLG1,EMC3

ATP5C1,ATP5F1,ATP5G3,ATP5L,C2orf47,PRADC1,COX5A,
COX5B,COX7A2,COX7A2L,DBI,FAM96A,MDH1,MEMO1,
MRPL11,MRPL22,MRPL35,NDUFS3,PDSS1,SDHD,SUCLG1
AK2,ATP5C1,ATPIF1,MPC2,C2orf47,CENPV,CRYL1,
FAM96A,GLOD4,IMP3,MGST2,MRPL48,MTCH2,NDUFC2,
OXNAD1,RARS2,SAR1B,SDHAF2,SDHB,SUCLG1,TMEM106C
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 SUCLG1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00139succinate-CoA ligase, alpha subunitapproved; nutraceuticalSuccinic acid


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Cross referenced IDs for SUCLG1
* 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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