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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SUCLA2 |
Basic gene info. | Gene symbol | SUCLA2 |
Gene name | succinate-CoA ligase, ADP-forming, beta subunit | |
Synonyms | A-BETA|MTDPS5|SCS-betaA | |
Cytomap | UCSC genome browser: 13q12.2-q13.3 | |
Genomic location | chr13 :48516790-48575462 | |
Type of gene | protein-coding | |
RefGenes | NM_003850.2, | |
Ensembl id | ENSG00000136143 | |
Description | ATP-specific succinyl-CoA synthetase subunit betaATP-specific succinyl-CoA synthetase, beta subunitmitochondrial succinyl-CoA ligase [ADP-forming] subunit betarenal carcinoma antigen NY-REN-39succinyl-CoA ligase [ADP-forming] subunit beta, mitochondri | |
Modification date | 20141219 | |
dbXrefs | MIM : 603921 | |
HGNC : HGNC | ||
Ensembl : ENSG00000136143 | ||
HPRD : 06798 | ||
Vega : OTTHUMG00000016889 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SUCLA2 | |
BioGPS: 8803 | ||
Gene Expression Atlas: ENSG00000136143 | ||
The Human Protein Atlas: ENSG00000136143 | ||
Pathway | NCI Pathway Interaction Database: SUCLA2 | |
KEGG: SUCLA2 | ||
REACTOME: SUCLA2 | ||
ConsensusPathDB | ||
Pathway Commons: SUCLA2 | ||
Metabolism | MetaCyc: SUCLA2 | |
HUMANCyc: SUCLA2 | ||
Regulation | Ensembl's Regulation: ENSG00000136143 | |
miRBase: chr13 :48,516,790-48,575,462 | ||
TargetScan: NM_003850 | ||
cisRED: ENSG00000136143 | ||
Context | iHOP: SUCLA2 | |
cancer metabolism search in PubMed: SUCLA2 | ||
UCL Cancer Institute: SUCLA2 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for SUCLA2(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SUCLA2 |
Familial Cancer Database: SUCLA2 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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/ |
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KEGG_PROPANOATE_METABOLISM REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: SUCLA2 |
MedGen: SUCLA2 (Human Medical Genetics with Condition) | |
ClinVar: SUCLA2 | |
Phenotype | MGI: SUCLA2 (International Mouse Phenotyping Consortium) |
PhenomicDB: SUCLA2 |
Mutations for SUCLA2 |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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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'. |
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- For Intra-chromosomal Variations |
There's no intra-chromosomal structural variation. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
pancreas | SUCLA2 | chr13 | 48529686 | 48529706 | chr23 | 67127938 | 67127958 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SUCLA2 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 |
BP397513 | SUCLA2 | 1 | 88 | 13 | 48516814 | 48516901 | C1orf86 | 88 | 500 | 1 | 2120990 | 2125256 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 1 |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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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Stat. for Non-Synonymous SNVs (# total SNVs=35) | (# total SNVs=7) |
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(# total SNVs=1) | (# total SNVs=0) |
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* 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 |
chr13:48528283-48528283 | p.D367N | 2 |
chr13:48528339-48528339 | p.V348G | 2 |
chr13:48563108-48563108 | p.D94Y | 2 |
chr13:48562731-48562731 | p.R160Q | 2 |
chr13:48542866-48542866 | p.L222L | 2 |
chr13:48528631-48528631 | p.I288M | 1 |
chr13:48571116-48571116 | p.V45I | 1 |
chr13:48542867-48542867 | p.L222P | 1 |
chr13:48523732-48523732 | p.A372T | 1 |
chr13:48562805-48562805 | p.M135I | 1 |
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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 |   | 9 | 1 |   | 2 |   | 1 |   |   | 3 | 2 |   |   |   | 4 | 2 |   | 5 |
# mutation |   | 2 |   | 8 | 1 |   | 2 |   | 1 |   |   | 3 | 2 |   |   |   | 4 | 2 |   | 5 |
nonsynonymous SNV |   | 1 |   | 7 | 1 |   | 1 |   | 1 |   |   | 3 | 2 |   |   |   |   | 2 |   | 5 |
synonymous SNV |   | 1 |   | 1 |   |   | 1 |   |   |   |   |   |   |   |   |   | 4 |   |   |   |
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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* 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 |
chr13:48542866 | p.L222L | 2 |
chr13:48562731 | p.R160Q | 2 |
chr13:48562805 | p.T253T | 1 |
chr13:48528531 | p.Q460R | 1 |
chr13:48563043 | p.L222P | 1 |
chr13:48517519 | p.D434Y | 1 |
chr13:48528631 | p.L408L | 1 |
chr13:48563071 | p.Q154E | 1 |
chr13:48523092 | p.R407W | 1 |
chr13:48528637 | p.T145P | 1 |
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* 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. |
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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 SUCLA2 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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AKAP11,COG3,COG6,DIS3,ELF1,FNDC3A,KBTBD7, GPALPP1,KPNA3,MTMR6,NAA16,NDFIP2,PDS5B,RB1, RBM26,RCBTB1,SUCLA2,UTP14C,VPS36,WBP4,ZC3H13 | ACAT1,AK3,ATPAF1,DLD,ETFDH,GHITM,GNPAT, HADHB,HOXA10,HSPB6,KAT2B,PARK2,PGM1,PHYH, PPP3CB,RDX,RRAGD,STRADB,SUCLA2,TBX15,ZAK | ||||
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ABHD13,ALG5,SPRYD7,MZT1,COG6,DIS3,MICU2, GPALPP1,KPNA3,MED4,MRPS31,NDFIP2,NUDT15,NUFIP1, PCID2,RNASEH2B,SAP18,SUCLA2,TGDS,UFM1,VPS36 | ATP5H,ATP5J,MINOS1,C9orf85,COX7C,DCUN1D1,ELMOD2, MGST2,MRPS36,MTCH2,PEX13,PPA2,PPIC,PRDX1, RPS27L,S100A14,SDHB,SUCLA2,SUMO1,TPRKB,TWF1 |
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* 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 |
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Pharmacological Information for SUCLA2 |
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DB Category | DB Name | DB's ID and Url link |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00139 | succinate-CoA ligase, ADP-forming, beta subunit | approved; nutraceutical | Succinic acid | ![]() | ![]() |
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Cross referenced IDs for SUCLA2 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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