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 MED24
Basic gene info.Gene symbolMED24
Gene namemediator complex subunit 24
SynonymsARC100|CRSP100|CRSP4|DRIP100|THRAP4|TRAP100
CytomapUCSC genome browser: 17q21.1
Genomic locationchr17 :38175349-38210889
Type of geneprotein-coding
RefGenesNM_001079518.1,
NM_001267797.1,NM_014815.3,NR_052017.1,
Ensembl idENSG00000008838
DescriptionCRSP complex subunit 4activator-recruited cofactor 100 kDa componentcofactor required for Sp1 transcriptional activation subunit 4cofactor required for Sp1 transcriptional activation, subunit 4, 100kDamediator of RNA polymerase II transcription subuni
Modification date20141207
dbXrefs MIM : 607000
HGNC : HGNC
Ensembl : ENSG00000008838
HPRD : 06107
Vega : OTTHUMG00000133329
ProteinUniProt: O75448
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MED24
BioGPS: 9862
Gene Expression Atlas: ENSG00000008838
The Human Protein Atlas: ENSG00000008838
PathwayNCI Pathway Interaction Database: MED24
KEGG: MED24
REACTOME: MED24
ConsensusPathDB
Pathway Commons: MED24
MetabolismMetaCyc: MED24
HUMANCyc: MED24
RegulationEnsembl's Regulation: ENSG00000008838
miRBase: chr17 :38,175,349-38,210,889
TargetScan: NM_001079518
cisRED: ENSG00000008838
ContextiHOP: MED24
cancer metabolism search in PubMed: MED24
UCL Cancer Institute: MED24
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for MED24(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MED24
Familial Cancer Database: MED24
* 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 607000; gene.
Orphanet
DiseaseKEGG Disease: MED24
MedGen: MED24 (Human Medical Genetics with Condition)
ClinVar: MED24
PhenotypeMGI: MED24 (International Mouse Phenotyping Consortium)
PhenomicDB: MED24

Mutations for MED24
* 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
* 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
pancreasMED24chr173821033438210354TNS4chr173864930038649320
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 MED24 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV410516MED241186173818970838189891MED24180383173818995138190154
BG957436EIF3CL1078162841255028412620MED2470462173817613838178965
BG108372SETD51492395099989510489MED24475566173817535538175446
BE465519UFD1L1233221943817019438402MED24232506173817656138178935
BE465526UFD1L1233221943817019438402MED24232515173817656138178944

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 # sample15  4      1   2  
GAIN (# sample)15  4      1   2  
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=59)
Stat. for Synonymous SNVs
(# total SNVs=38)
Stat. for Deletions
(# total SNVs=8)
Stat. for Insertions
(# total SNVs=1)

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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
chr17:38178256-38178256p.R859*4
chr17:38178659-38178659p.R837R3
chr17:38176550-38176550p.R894W3
chr17:38191512-38191512p.A139A3
chr17:38179414-38179414p.G740G2
chr17:38188941-38188941p.G299G2
chr17:38189655-38189655p.N205I2
chr17:38179620-38179620p.R672C2
chr17:38183692-38183692p.L492L2
chr17:38209742-38209742p.W37L2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample54 8  4 211563  67 17
# mutation56 9  4 211563  67 19
nonsynonymous SNV34 6  4 2  242  34 11
synonymous SNV22 3     11321  33 8
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
chr17:38209742p.W37L,MED243
chr17:38179414p.G727G,MED242
chr17:38178659p.R824R,MED242
chr17:38182435p.E941K,MED241
chr17:38189629p.E523K,MED241
chr17:38176104p.A275G,MED241
chr17:38183243p.A81T1
chr17:38192383p.T80A1
chr17:38178692p.E916E,MED241
chr17:38187823p.G709C,MED241

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 MED24 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 MED24

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

MIEN1,C2orf54,CASC3,CDC6,CDK12,ERBB2,FBXL20,
GRB7,GSDMB,MED1,MED24,MSL1,ORMDL3,PGAP3,
PPP1R1B,PSMD3,RARA,SMARCE1,STARD3,THRA,WIPF2
AHDC1,ATXN7L2,CNKSR1,DPH2,FOXK2,HEATR2,HMGA1,
MED24,MYBBP1A,PPP2R4,PRMT1,RNF31,RRP12,SBK1,
SLC37A4,SMARCD3,MIEF2,TBRG4,TMEM201,UBQLN4,WNK2

AATF,MIEN1,CASC3,ERBB2,FXYD2,GRB7,KCNA10,
MED24,MSL1,ORMDL3,PGAP3,PPP1R1B,PSMD3,RAPGEFL1,
RGSL1,RPL19,SNAR-A2,STARD3,TCAP,THRA,UGT1A6
CHAF1A,CHTF18,DAZAP1,DDX54,DIS3L2,EFTUD2,HNRNPM,
CLUH,LMNB2,LRRC45,MED24,NBEAL2,NCLN,TONSL,
PAXIP1,PTBP1,RECQL4,SRRT,SYMPK,TTLL4,VARS
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 MED24


There's no related Drug.
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Cross referenced IDs for MED24
* 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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