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 MED15
Basic gene info.Gene symbolMED15
Gene namemediator complex subunit 15
SynonymsARC105|CAG7A|CTG7A|PCQAP|TIG-1|TIG1|TNRC7
CytomapUCSC genome browser: 22q11.2
Genomic locationchr22 :20861885-20941919
Type of geneprotein-coding
RefGenesNM_001003891.2,
NM_001293234.1,NM_001293235.1,NM_001293236.1,NM_001293237.1,
NM_015889.4,
Ensembl idENSG00000099917
DescriptionCTG repeat protein 7aPC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated proteinPC2 glutamine/Q-rich-associated proteinPC2-glutamine-rich-associated proteinTPA inducible gene-1TPA inducible proteinTPA-inducible gene 1 protein
Modification date20141207
dbXrefs MIM : 607372
HGNC : HGNC
Ensembl : ENSG00000099917
HPRD : 12117
Vega : OTTHUMG00000150810
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MED15
BioGPS: 51586
Gene Expression Atlas: ENSG00000099917
The Human Protein Atlas: ENSG00000099917
PathwayNCI Pathway Interaction Database: MED15
KEGG: MED15
REACTOME: MED15
ConsensusPathDB
Pathway Commons: MED15
MetabolismMetaCyc: MED15
HUMANCyc: MED15
RegulationEnsembl's Regulation: ENSG00000099917
miRBase: chr22 :20,861,885-20,941,919
TargetScan: NM_001003891
cisRED: ENSG00000099917
ContextiHOP: MED15
cancer metabolism search in PubMed: MED15
UCL Cancer Institute: MED15
Assigned class in ccmGDBC

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Phenotypic Information for MED15(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MED15
Familial Cancer Database: MED15
* 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: MED15
MedGen: MED15 (Human Medical Genetics with Condition)
ClinVar: MED15
PhenotypeMGI: MED15 (International Mouse Phenotyping Consortium)
PhenomicDB: MED15

Mutations for MED15
* 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
ovaryMED15chr222089436020894380KLHL22chr222082883020828850
ovaryMED15chr222090209120902111chr221963232119632341
ovaryMED15chr222092014620920166MED15chr222092258220922602
pancreasMED15chr222087973120879751chr222101892821018948
pancreasMED15chr222091532320915343MED15chr222091580420915824
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 MED15 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI051034MED155110222093946020939565MED15106165222093940320939462
CF125171RPN21104203583573935835842MED1597666222086195820918847
DB259160FAM46A118068246221782462396MED15175579222093700820938693
BG003281EWSR1364222969568529695746MED1553210222092898220929139
DB193761RPLP2124511809968811645MED15240477222092284820937156
BF999641MED151163222092372320923885MED15159454222092872020929015
BG003287EWSR1869222969568529695746MED1558215222092898220929139
BG003288EWSR11172222969568529695746MED1561217222092898220929139
BF991563MED1515134222092883820928959TRIM40128178614453881445438

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 # sample    1   1 1  1  2
GAIN (# sample)        1 1  1  2
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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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=30)
Stat. for Synonymous SNVs
(# total SNVs=18)
Stat. for Deletions
(# total SNVs=5)
Stat. for Insertions
(# total SNVs=9)

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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
chr22:20920813-20920814p.Q250_Q251insQ8
chr22:20918916-20918918p.Q211delQ3
chr22:20920813-20920813p.Q250Q2
chr22:20937642-20937642p.M566I2
chr22:20937674-20937674p.S577L2
chr22:20929471-20929471p.S408S2
chr22:20918750-20918750p.L155L2
chr22:20918772-20918772p.Q163*2
chr22:20905758-20905758p.I64I2
chr22:20939265-20939265p.V643I1

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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
# sample41 41 1 3  62  267 11
# mutation41 41 1 3  62  268 13
nonsynonymous SNV41 21 1 1  51  235 9
synonymous SNV   2    2  11   33 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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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
chr22:20929471p.S466L,MED152
chr22:20937674p.S408S2
chr22:20918760p.R551Q,MED151
chr22:20939198p.P203P,MED151
chr22:20921084p.P416S1
chr22:20936973p.R553H,MED151
chr22:20920816p.P211S,MED151
chr22:20939211p.L417S1
chr22:20921087p.I563I,MED151
chr22:20937171p.P216S,MED151

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 MED15 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 MED15

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

ARHGEF1,ARVCF,CDPF1,DGCR14,DGCR2,DGCR6L,GGA1,
KLHL22,LZTR1,MED15,MKL1,NOL12,PPIL2,PRR5,
TBC1D22A,THAP7,TOP3B,TRIOBP,TRMT2A,YDJC,ZDHHC8
BTBD2,TMEM259,BRAT1,HGS,AP5Z1,LMF2,LZTS2,
MAP3K11,MBD3,MED15,NCLN,PLCB3,PNPLA6,RANBP3,
SH3GL1,SIPA1,SLC39A13,SLC4A2,STRN4,VAC14,ZDHHC8

AP1B1,BCAR1,BCR,GUCD1,PRR14L,KIAA0930,CYB5R3,
DGCR14,DGCR2,GGA1,GTPBP1,LMF2,MED15,MKL1,
MYH9,PLEC,PLXNB2,PPIL2,RHOF,TBC1D22A,TOM1
AP2A1,ELMSAN1,FLII,GBF1,ARHGAP35,KDM2A,KSR1,
MED15,NDST1,NFE2L1,OTUD7B,PI4KA,PLXNB2,RAPGEF1,
SOX13,TAOK2,UBR4,ZFYVE26,ZGPAT,ZMIZ1,ZNF592
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 MED15


There's no related Drug.
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Cross referenced IDs for MED15
* 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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