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 MED23
Basic gene info.Gene symbolMED23
Gene namemediator complex subunit 23
SynonymsARC130|CRSP130|CRSP133|CRSP3|DRIP130|MRT18|SUR-2|SUR2
CytomapUCSC genome browser: 6q22.33-q24.1
Genomic locationchr6 :131895105-131949363
Type of geneprotein-coding
RefGenesNM_001270521.1,
NM_001270522.1,NM_004830.3,NM_015979.3,
Ensembl idENSG00000112282
Description130 kDa transcriptional co-activator133 kDa transcriptional co-activatoractivator-recruited cofactor 130 kDa componentcofactor required for Sp1 transcriptional activation subunit 3mediator of RNA polymerase II transcription subunit 23vitamin D3 recep
Modification date20141207
dbXrefs MIM : 605042
HGNC : HGNC
Ensembl : ENSG00000112282
HPRD : 05436
Vega : OTTHUMG00000015565
ProteinUniProt: Q9ULK4
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MED23
BioGPS: 9439
Gene Expression Atlas: ENSG00000112282
The Human Protein Atlas: ENSG00000112282
PathwayNCI Pathway Interaction Database: MED23
KEGG: MED23
REACTOME: MED23
ConsensusPathDB
Pathway Commons: MED23
MetabolismMetaCyc: MED23
HUMANCyc: MED23
RegulationEnsembl's Regulation: ENSG00000112282
miRBase: chr6 :131,895,105-131,949,363
TargetScan: NM_001270521
cisRED: ENSG00000112282
ContextiHOP: MED23
cancer metabolism search in PubMed: MED23
UCL Cancer Institute: MED23
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for MED23(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MED23
Familial Cancer Database: MED23
* 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 BRCA 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 605042; gene.
605042; gene.
614249; phenotype.
614249; phenotype.
Orphanet 88616; Autosomal recessive non-syndromic intellectual disability.
88616; Autosomal recessive non-syndromic intellectual disability.
DiseaseKEGG Disease: MED23
MedGen: MED23 (Human Medical Genetics with Condition)
ClinVar: MED23
PhenotypeMGI: MED23 (International Mouse Phenotyping Consortium)
PhenomicDB: MED23

Mutations for MED23
* 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
There's no inter-chromosomal structural variation.
- 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
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 MED23 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN388362MMP141363142330580823305858MED23552756131908097131908317
AA648640MED235956131932398131932488MED23894346131932481131932825
AA721515MED237976131932398131932488MED23914696131932481131932859
AA648178MED236966131932398131932488MED23904066131932481131932798
BQ223279MED2343986131910602131910657MED23978796131908205131908986
AW363299MED2320896131930300131930370MED23746446131931103131931678

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=75)
Stat. for Synonymous SNVs
(# total SNVs=19)
Stat. for Deletions
(# total SNVs=12)
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
chr6:131912472-131912472p.Q1223*3
chr6:131919885-131919885p.N746fs*113
chr6:131921249-131921249p.Q717*3
chr6:131944520-131944520p.R123W2
chr6:131937037-131937037p.?2
chr6:131929091-131929091p.D400N2
chr6:131908944-131908944p.R1328C2
chr6:131925356-131925356p.Y573C2
chr6:131912565-131912565p.D1192Y2
chr6:131911468-131911468p.M1267I2

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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
# sample15 13  7 3  85   813113
# mutation15 16  7 3  85   816114
nonsynonymous SNV15 12  4 2  44   410111
synonymous SNV   4  3 1  41   46 3
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
chr6:131912565p.D1192Y,MED233
chr6:131929091p.D400N,MED232
chr6:131931276p.L329L,MED232
chr6:131944545p.H454R,MED231
chr6:131914170p.I237V,MED231
chr6:131926396p.G50S,MED231
chr6:131917269p.R1265H,MED231
chr6:131911475p.L1075L,MED231
chr6:131921227p.P724H,MED231
chr6:131939618p.S450S,MED231

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 MED23 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 MED23

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

AIM1,AKAP7,ASCC3,ATG5,BCLAF1,C6orf203,ENPP1,
GOLGA1,HBS1L,LATS1,LOC100129034,MED23,NEDD1,PDSS2,
PREP,QRSL1,SCAF8,RTN4IP1,SENP6,SHPRH,STX7
ARID2,MMS22L,TBC1D32,CCNT2,CD2AP,CNOT6,DCAF17,
MED23,PHF6,PPIP5K2,RBM26,SMARCAD1,TRIM33,USP37,
WRN,ZBTB26,ZNF24,ZNF260,ZNF417,ZNF518A,ZNF91

BAZ2B,CDK19,DOPEY1,ERCC6,FAM120B,FBXL4,GOPC,
HEATR5B,GLTSCR1L,UFL1,KLHL24,LATS1,MED23,PHC3,
PHF3,RASA2,SCAF8,SENP6,SHPRH,TAB2,ZNF292
CEP192,CMTM4,DOPEY2,ERCC6,HEATR5B,HOXA6,JRKL,
KIAA1147,LIMD1,MBTD1,MED23,NFYA,PHLPP1,PTCH1,
TTC17,ZCCHC8,ZFP62,ZKSCAN1,ZNF141,ZNF41,ZNF81
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 MED23


There's no related Drug.
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Cross referenced IDs for MED23
* 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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