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 MED22
Basic gene info.Gene symbolMED22
Gene namemediator complex subunit 22
SynonymsMED24|SURF5|surf-5
CytomapUCSC genome browser: 9q34.2
Genomic locationchr9 :136207754-136214972
Type of geneprotein-coding
RefGenesNM_133640.4,
NM_181491.2,NM_006752.4,
Ensembl idENSG00000261579
Descriptionmediator of RNA polymerase II transcription subunit 22surfeit locus protein 5
Modification date20141207
dbXrefs MIM : 185641
HGNC : HGNC
Ensembl : ENSG00000148297
HPRD : 01713
Vega : OTTHUMG00000020869
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MED22
BioGPS: 6837
Gene Expression Atlas: ENSG00000261579
The Human Protein Atlas: ENSG00000261579
PathwayNCI Pathway Interaction Database: MED22
KEGG: MED22
REACTOME: MED22
ConsensusPathDB
Pathway Commons: MED22
MetabolismMetaCyc: MED22
HUMANCyc: MED22
RegulationEnsembl's Regulation: ENSG00000261579
miRBase: chr9 :136,207,754-136,214,972
TargetScan: NM_133640
cisRED: ENSG00000261579
ContextiHOP: MED22
cancer metabolism search in PubMed: MED22
UCL Cancer Institute: MED22
Assigned class in ccmGDBC

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Phenotypic Information for MED22(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MED22
Familial Cancer Database: MED22
* 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: MED22
MedGen: MED22 (Human Medical Genetics with Condition)
ClinVar: MED22
PhenotypeMGI: MED22 (International Mouse Phenotyping Consortium)
PhenomicDB: MED22

Mutations for MED22
* 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 MED22 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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr9:136211103-136211103p.A97V1
chr9:136211113-136211113p.V94M1
chr9:136212036-136212036p.A65A1
chr9:136210997-136210997p.E132E1
chr9:136212099-136212099p.D44D1
chr9:136211030-136211030p.D121D1
chr9:136212104-136212104p.E43Q1
chr9:136211045-136211045p.L116L1
chr9:136213393-136213393p.?1
chr9:136211062-136211062p.E111K1

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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
# sample22 11 1 1  111  13 3
# mutation22 11 1 1  111  13 4
nonsynonymous SNV12 11 1    111   3  
synonymous SNV1       1       1  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
chr9:136208458p.S167L2
chr9:136211100p.L166R1
chr9:136211103p.Q3Q,MED221
chr9:136211174p.E143A1
chr9:136212036p.E132E,MED221
chr9:136208461p.L116L,MED221
chr9:136212099p.E110K,MED221
chr9:136208530p.L108L,MED221
chr9:136212104p.R101H,MED221
chr9:136210997p.I98T,MED221

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 MED22 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 MED22

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

ANAPC2,ASB6,C9orf114,C9orf69,RABL6,CIZ1,NELFB,
FAM73B,FBXW5,PPP1R26,MED22,PMPCA,POMT1,REXO4,
SDCCAG3,SNAPC4,SURF6,TRAF2,UBAC1,USP20,WDR5
ALKBH4,ARFGAP1,ARMC7,C19orf25,SMG9,CCDC102A,DDX41,
EHMT2,GHDC,LOC148413,MAN1B1,MED22,MOGS,NAT9,
NDOR1,RANBP3,SLC12A9,TRIM11,USP20,WDR46,XAB2

ABL1,PRRC2B,BRD3,C9orf69,CDK5RAP2,CEP250,CIZ1,
NELFB,EHMT1,GIGYF1,MED22,NOTCH1,NUP214,RAPGEF1,
REXO4,SNAPC4,TBC1D13,TRAF2,USP20,VAV2,WDR5
ABCA3,CCDC102A,COL8A2,CRTC3,FAM117A,FNBP1,FOXJ2,
FRMD4A,HEATR6,LOXL1,MAGEE1,MECP2,MED22,NFIX,
PACS1,PKN1,RANBP3,SOX12,ST5,STAT5B,TLN1
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 MED22


There's no related Drug.
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Cross referenced IDs for MED22
* 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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