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 SLC25A20
Basic gene info.Gene symbolSLC25A20
Gene namesolute carrier family 25 (carnitine/acylcarnitine translocase), member 20
SynonymsCAC|CACT
CytomapUCSC genome browser: 3p21.31
Genomic locationchr3 :48894355-48936426
Type of geneprotein-coding
RefGenesNM_000387.5,
Ensembl idENSG00000178537
Descriptionmitochondrial carnitine/acylcarnitine carrier protein
Modification date20141207
dbXrefs MIM : 613698
HGNC : HGNC
Ensembl : ENSG00000178537
HPRD : 01953
Vega : OTTHUMG00000133538
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC25A20
BioGPS: 788
Gene Expression Atlas: ENSG00000178537
The Human Protein Atlas: ENSG00000178537
PathwayNCI Pathway Interaction Database: SLC25A20
KEGG: SLC25A20
REACTOME: SLC25A20
ConsensusPathDB
Pathway Commons: SLC25A20
MetabolismMetaCyc: SLC25A20
HUMANCyc: SLC25A20
RegulationEnsembl's Regulation: ENSG00000178537
miRBase: chr3 :48,894,355-48,936,426
TargetScan: NM_000387
cisRED: ENSG00000178537
ContextiHOP: SLC25A20
cancer metabolism search in PubMed: SLC25A20
UCL Cancer Institute: SLC25A20
Assigned class in ccmGDBC

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Phenotypic Information for SLC25A20(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC25A20
Familial Cancer Database: SLC25A20
* 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_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC25A20
MedGen: SLC25A20 (Human Medical Genetics with Condition)
ClinVar: SLC25A20
PhenotypeMGI: SLC25A20 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC25A20

Mutations for SLC25A20
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasSLC25A20chr34893046148930481chr174137435141374371
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 SLC25A20 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

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=19)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr3:48921465-48921465p.K97N2
chr3:48929501-48929501p.R37Q2
chr3:48916844-48916844p.V122I2
chr3:48896629-48896629p.S205N1
chr3:48896993-48896993p.G201G1
chr3:48921496-48921496p.A87V1
chr3:48897000-48897000p.P199L1
chr3:48921505-48921505p.P84L1
chr3:48897041-48897041p.M185I1
chr3:48921519-48921519p.I79I1

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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 1 3  2 2  32  144 4
# mutation 1 3  2 2  32  144 4
nonsynonymous SNV 1 2  1 1  21  113 4
synonymous SNV   1  1 1  11   31  
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
chr3:48916844p.V122I2
chr3:48896629p.P199L1
chr3:48921496p.Q39P1
chr3:48896993p.M185I1
chr3:48921519p.R37L1
chr3:48897000p.F163F1
chr3:48921537p.E162E1
chr3:48897041p.Q161Q1
chr3:48921538p.Q141E1
chr3:48900021p.G117W1

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 SLC25A20 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 SLC25A20

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

ABHD14B,APEH,BECN1,C3orf18,CCDC51,CYB561D2,MLH1,
NICN1,NPRL2,PDHB,PRKCD,QRICH1,RFT1,RHOA,
RNF123,SACM1L,SEC22C,SLC25A20,SPCS1,TCTA,TUSC2
BTBD6,NATD1,C22orf39,CYSTM1,CCDC69,CD99L2,EIF2B3,
GPI,ITGA7,MAP2K1,MGST3,MSRB2,NKAPL,PPP1R1A,
RILP,RTN4,SERPINF1,SLC25A20,TTC7B,UGP2,YWHAG

ACOT11,ACVRL1,ATP6V0D1,BPNT1,BTNL3,CA4,CCRL2,
CDHR5,DOK4,ETFDH,RMDN2,LRRC19,SLC51B,SGK2,
SLC22A18AS,SLC25A20,SLC25A34,SLC46A3,TMEM150B,TMEM37,TMEM82
BPNT1,CYSTM1,ABRACL,CALML4,CCL15,EAPP,HTATIP2,
IL10RB,LRRC19,MAD2L1BP,MGST3,MYL12B,NAT2,NDFIP2,
SLC51B,SAT1,SLC25A20,SLC25A5,SLC35D2,VAMP8,WSB2
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 SLC25A20
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
DB00583solute carrier family 25 (carnitine/acylcarnitine translocase), member 20approvedL-Carnitine


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Cross referenced IDs for SLC25A20
* 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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