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 MED16
Basic gene info.Gene symbolMED16
Gene namemediator complex subunit 16
SynonymsDRIP92|THRAP5|TRAP95
CytomapUCSC genome browser: 19p13.3
Genomic locationchr19 :867961-893218
Type of geneprotein-coding
RefGenesNM_005481.2,
Ensembl idENSG00000175221
Descriptionmediator of RNA polymerase II transcription subunit 16thyroid hormone receptor-associated protein 5thyroid hormone receptor-associated protein complex 95 kDa componentthyroid hormone receptor-associated protein, 95-kD subunitvitamin D3 receptor-intera
Modification date20141207
dbXrefs MIM : 604062
HGNC : HGNC
Ensembl : ENSG00000175221
HPRD : 06816
Vega : OTTHUMG00000181841
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MED16
BioGPS: 10025
Gene Expression Atlas: ENSG00000175221
The Human Protein Atlas: ENSG00000175221
PathwayNCI Pathway Interaction Database: MED16
KEGG: MED16
REACTOME: MED16
ConsensusPathDB
Pathway Commons: MED16
MetabolismMetaCyc: MED16
HUMANCyc: MED16
RegulationEnsembl's Regulation: ENSG00000175221
miRBase: chr19 :867,961-893,218
TargetScan: NM_005481
cisRED: ENSG00000175221
ContextiHOP: MED16
cancer metabolism search in PubMed: MED16
UCL Cancer Institute: MED16
Assigned class in ccmGDBC

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Phenotypic Information for MED16(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MED16
Familial Cancer Database: MED16
* 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: MED16
MedGen: MED16 (Human Medical Genetics with Condition)
ClinVar: MED16
PhenotypeMGI: MED16 (International Mouse Phenotyping Consortium)
PhenomicDB: MED16

Mutations for MED16
* 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
pancreasMED16chr19887889887909MED16chr19892119892139
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 MED16 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM919198MED1616019879940879999MED165440219884903886012
BM825118CFD19619861861861956MED169562719871050873584
BF766064RBFOX2161223613728036137340MED165823519876403876580

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  
GAIN (# sample)              1  
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=36)
Stat. for Synonymous SNVs
(# total SNVs=25)
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
chr19:871135-871135p.V739V5
chr19:879947-879947p.S448N5
chr19:871222-871222p.D710D5
chr19:875275-875279p.R579fs*133
chr19:871987-871987p.T679T3
chr19:875402-875402p.P538L2
chr19:891068-891068p.E22K2
chr19:875447-875447p.S523F2
chr19:873482-873482p.F624F2
chr19:879943-879943p.H449Q2

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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
# sample31141 3 2  731119913
# mutation31141 3 2  7311181013
nonsynonymous SNV21 4  2 1  511116812
synonymous SNV1 1 1 1 1  22   22 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
chr19:868150p.P862L2
chr19:877145p.R647R1
chr19:872058p.S498I1
chr19:885838p.D256N1
chr19:873579p.S637F1
chr19:890996p.D490A1
chr19:879980p.S247S1
chr19:872062p.F624F1
chr19:885852p.H463H1
chr19:875283p.V246M1

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 MED16 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 MED16

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

ALKBH7,BTBD2,TPGS1,C19orf25,TMEM259,ABHD17A,MZT2B,
FBXL15,MBD3,MED16,NDUFS7,PIN1,PLEKHJ1,POLR2E,
POLRMT,RPS15,SLC39A3,SPPL2B,STK11,UBXN6,WDR18
ARMC5,BCL2L12,C9orf114,E4F1,FARSA,FZR1,HSPBP1,
IRF2BP1,LRWD1,MED16,NDOR1,PICK1,RUVBL2,TBL3,
TRIM28,NELFA,XAB2,YIPF2,ZBTB45,ZNF408,ZNF653

ADAT3,AES,ATG4D,TMEM259,CSNK1G2,ABHD17A,FKBP8,
FZR1,KEAP1,LRFN3,MAP2K2,MED16,MPND,NDUFS7,
NR2F6,RAB11B,REXO1,RNF126,STK11,UBXN6,ZNF653
ADAT3,ARAF,BCAR1,C6orf132,TOR4A,CTDP1,EFNA2,
FAM83H,FURIN,GMEB2,KLF16,MAP3K11,MED16,METRNL,
PAK4,PPP1R13L,RAVER1,TMEM115,TRIM11,ZC3H3,ZNF787
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 MED16


There's no related Drug.
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Cross referenced IDs for MED16
* 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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