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 MED1
Basic gene info.Gene symbolMED1
Gene namemediator complex subunit 1
SynonymsCRSP1|CRSP200|DRIP205|DRIP230|PBP|PPARBP|PPARGBP|RB18A|TRAP220|TRIP2
CytomapUCSC genome browser: 17q12
Genomic locationchr17 :37560537-37607527
Type of geneprotein-coding
RefGenesNM_004774.3,
Ensembl idENSG00000125686
DescriptionARC205PPAR binding proteinPPAR-binding proteinPPARG binding proteinTR-interacting protein 2TRIP-2activator-recruited cofactor 205 kDa componentmediator of RNA polymerase II transcription subunit 1p53 regulatory protein RB18Aperoxisome proliferato
Modification date20141207
dbXrefs MIM : 604311
HGNC : HGNC
Ensembl : ENSG00000125686
HPRD : 05055
Vega : OTTHUMG00000133216
ProteinUniProt: Q15648
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MED1
BioGPS: 5469
Gene Expression Atlas: ENSG00000125686
The Human Protein Atlas: ENSG00000125686
PathwayNCI Pathway Interaction Database: MED1
KEGG: MED1
REACTOME: MED1
ConsensusPathDB
Pathway Commons: MED1
MetabolismMetaCyc: MED1
HUMANCyc: MED1
RegulationEnsembl's Regulation: ENSG00000125686
miRBase: chr17 :37,560,537-37,607,527
TargetScan: NM_004774
cisRED: ENSG00000125686
ContextiHOP: MED1
cancer metabolism search in PubMed: MED1
UCL Cancer Institute: MED1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for MED1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MED1
Familial Cancer Database: MED1
* 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 604311; gene.
Orphanet
DiseaseKEGG Disease: MED1
MedGen: MED1 (Human Medical Genetics with Condition)
ClinVar: MED1
PhenotypeMGI: MED1 (International Mouse Phenotyping Consortium)
PhenomicDB: MED1

Mutations for MED1
* 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
breastMED1chr173759406137594061chr173807564138075641
breastMED1chr173760477537604775chr174109931241099312
breastMED1chr173760686337607263WIPF2chr173839866738399067
pancreasMED1chr173759646137596481chr174655042846550448
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 MED1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE818200DNAJC525194206256596462566133MED1185539173756359737563951
H19757MED11480173756557237565638HPCAL46830414014465340144881
H21133MED1268173756557237565638HPCAL45629114014465540144881

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 # sample10     1 2     2  
GAIN (# sample)10     1 2     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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=88)
Stat. for Synonymous SNVs
(# total SNVs=22)
Stat. for Deletions
(# total SNVs=4)
Stat. for Insertions
(# total SNVs=0)
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
chr17:37566456-37566456p.S673F3
chr17:37565611-37565611p.G955S2
chr17:37566882-37566882p.T531I2
chr17:37565455-37565455p.D1007H2
chr17:37566511-37566511p.Q655E2
chr17:37587411-37587411p.K202N2
chr17:37563791-37563791p.S1561R2
chr17:37566444-37566444p.R677H2
chr17:37563898-37563898p.H1526D2
chr17:37564239-37564239p.K1412R2

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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
# sample61316  7 32 1391111012 8
# mutation71317  9 32 13111111013 12
nonsynonymous SNV61313  8 21 10811187 11
synonymous SNV1  4  1 11 33   26 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
chr17:37564132p.P1448S2
chr17:37587411p.G955G2
chr17:37565966p.K202N2
chr17:37565609p.R677H2
chr17:37566444p.T836T2
chr17:37563981p.S588L1
chr17:37565297p.S314S1
chr17:37566692p.S1239L1
chr17:37564497p.H1024Y1
chr17:37565808p.P834P1

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 MED1 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 MED1

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

ATP1A1,C11orf31,ATP1A1-AS1,CD58,CDH19,CLP1,CTNND1,
GDAP2,KCTD14,LCN2,MED19,OR6C70,OR6Q1,PLSCR5,
PRG2,SLC43A3,TIMM10,TMX2,VTCN1,WDR3,ZDHHC5
APOA1BP,ARF5,BUD31,C12orf57,C17orf49,CUTA,DPCD,
MED19,MED27,OVCA2,PDCD6,PHF5A,PRELID1,RAB34,
SDF2,SF3B5,SNRPF,TMEM208,UFC1,VPS25,ZNRD1

ASNA1,ATP5L,BANF1,C11orf31,LAMTOR1,COA4,FAU,
MED19,MRPL11,MRPL21,MRPL49,MRPL54,NDUFS3,POLR2G,
PPP1CA,SDHAF2,TIMM8B,TMEM223,TRMT112,TTC9C,YIF1A
ASNA1,ATP6V0B,BID,BUD31,C1orf174,TIMMDC1,TMEM261,
CHCHD2,DCTPP1,DPM3,FAM58A,FAM96B,LSM7,LYRM2,
MED19,MRPL54,NDUFA7,RPSAP58,SERF2,SSR2,STOML2
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 MED1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA33556; -.
Organism-specific databasesCTD 5469; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB08696mediator complex subunit 1experimental5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL
DB00755mediator complex subunit 1approved; nutraceutical; investigationalTretinoin


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Cross referenced IDs for MED1
* 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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