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 MED18
Basic gene info.Gene symbolMED18
Gene namemediator complex subunit 18
Synonymsp28b
CytomapUCSC genome browser: 1p35.3
Genomic locationchr1 :28655512-28662478
Type of geneprotein-coding
RefGenesNM_001127350.1,
NM_017638.2,
Ensembl idENSG00000130772
DescriptionTRAP/mediator complex subunit p28bmediator of RNA polymerase II transcription subunit 18mediator of RNA polymerase II transcription, subunit 18 homolog
Modification date20141207
dbXrefs MIM : 612384
HGNC : HGNC
Ensembl : ENSG00000130772
HPRD : 17476
Vega : OTTHUMG00000003537
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MED18
BioGPS: 54797
Gene Expression Atlas: ENSG00000130772
The Human Protein Atlas: ENSG00000130772
PathwayNCI Pathway Interaction Database: MED18
KEGG: MED18
REACTOME: MED18
ConsensusPathDB
Pathway Commons: MED18
MetabolismMetaCyc: MED18
HUMANCyc: MED18
RegulationEnsembl's Regulation: ENSG00000130772
miRBase: chr1 :28,655,512-28,662,478
TargetScan: NM_001127350
cisRED: ENSG00000130772
ContextiHOP: MED18
cancer metabolism search in PubMed: MED18
UCL Cancer Institute: MED18
Assigned class in ccmGDBC

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Phenotypic Information for MED18(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MED18
Familial Cancer Database: MED18
* 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: MED18
MedGen: MED18 (Human Medical Genetics with Condition)
ClinVar: MED18
PhenotypeMGI: MED18 (International Mouse Phenotyping Consortium)
PhenomicDB: MED18

Mutations for MED18
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MED18 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=18)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr1:28660972-28660972p.R40C2
chr1:28661303-28661303p.R150H2
chr1:28661169-28661169p.C105C1
chr1:28661311-28661311p.V153L1
chr1:28657194-28657194p.T7T1
chr1:28661170-28661170p.V106M1
chr1:28661339-28661339p.A162V1
chr1:28660959-28660959p.L35L1
chr1:28661205-28661205p.F117L1
chr1:28661359-28661359p.V169M1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample  13  1 4   2   23 4
# mutation  23  1 4   2   23 4
nonsynonymous SNV  12  1 3   2   12 3
synonymous SNV  11    1       11 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
chr1:28661170p.E20K,MED181
chr1:28657231p.R150H,MED181
chr1:28661175p.S31I,MED181
chr1:28660946p.E161K,MED181
chr1:28661233p.L35L,MED181
chr1:28660959p.V169M,MED181
chr1:28661264p.R40C,MED181
chr1:28660972p.K205N,MED181
chr1:28661297p.L52F,MED181
chr1:28661008p.L70L,MED181

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 MED18 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 MED18

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

AKR7A2,APITD1,ATPIF1,MINOS1,KDF1,COQ4,DNAJC8,
FLJ37453,GPATCH3,GPN2,HMGCL,IQCC,MED18,NMNAT1,
NUDC,PARK7,PEF1,PIGV,TAF12,TMEM222,TRNAU1AP
AGER,BRICD5,C1orf174,FAM225A,CYB561D1,INPP5E,LMBR1L,
MED18,MTHFR,PGPEP1,TBCC,IGFLR1,TMEM150A,TNFRSF25,
USF1,USP21,XKR8,ZBTB3,ZGLP1,ZSWIM1,ZSWIM3

GSKIP,C14orf142,KDF1,ELP6,CDC42,CNIH1,COMMD3,
FAM118B,GTF2B,HIGD1A,MED18,MED31,MRPL54,PPP1R8,
SAR1B,SCO2,SEP15,SNRNP40,TRNAU1AP,TSPO,TXNL1
ARF5,ATP6V0B,ATPIF1,BLOC1S1,LAMTOR1,C15orf48,MIEN1,
LAMTOR4,COA3,COX4I1,COX6A1,EAPP,MED18,MRPL14,
NDUFA2,PDCD6,PDZD11,PPCS,STK16,TMEM106C,ZNHIT1
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 MED18


There's no related Drug.
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Cross referenced IDs for MED18
* 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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