Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 MED13L
Basic gene info.Gene symbolMED13L
Gene namemediator complex subunit 13-like
SynonymsPROSIT240|THRAP2|TRAP240L
CytomapUCSC genome browser: 12q24.21
Genomic locationchr12 :116396380-116714991
Type of geneprotein-coding
RefGenesNM_015335.4,
Ensembl idENSG00000123066
Descriptionmediator of RNA polymerase II transcription subunit 13-likethyroid hormone receptor-associated protein 2thyroid hormone receptor-associated protein complex 240 kDa component-like
Modification date20141207
dbXrefs MIM : 608771
HGNC : HGNC
HPRD : 10579
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MED13L
BioGPS: 23389
Gene Expression Atlas: ENSG00000123066
The Human Protein Atlas: ENSG00000123066
PathwayNCI Pathway Interaction Database: MED13L
KEGG: MED13L
REACTOME: MED13L
ConsensusPathDB
Pathway Commons: MED13L
MetabolismMetaCyc: MED13L
HUMANCyc: MED13L
RegulationEnsembl's Regulation: ENSG00000123066
miRBase: chr12 :116,396,380-116,714,991
TargetScan: NM_015335
cisRED: ENSG00000123066
ContextiHOP: MED13L
cancer metabolism search in PubMed: MED13L
UCL Cancer Institute: MED13L
Assigned class in ccmGDBC

Top
Phenotypic Information for MED13L(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MED13L
Familial Cancer Database: MED13L
* 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: MED13L
MedGen: MED13L (Human Medical Genetics with Condition)
ClinVar: MED13L
PhenotypeMGI: MED13L (International Mouse Phenotyping Consortium)
PhenomicDB: MED13L

Mutations for MED13L
* 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
breastMED13Lchr12116451691116451691MED13Lchr12116476980116476980
ovaryMED13Lchr12116401464116401484chr223764732737647347
ovaryMED13Lchr12116427802116427822chr12113947591113947611
ovaryMED13Lchr12116564989116565009MED13Lchr12116565502116565522
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 MED13L related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CK824480MED13L3314012116558166116558273SERPINI21365223167173569167173955
BF934070MED13L1325012116595421116595660MAP1B24749857150407171504322
BF357082MED13L126512116666969116667232PTPN2326027934743946747439486
AW809452HEATR21614347776821777229MED13L43156912116578385116578523
AA502152MED13L112312116441537116441659MED13L11531212116441733116441930
CK824479SERPINI215163167173440167173955MED13L51258612116558166116558240
BG988299MED13L16512116403886116403951GTPBP4553041010564101058602
DA392149MED13L150112116398992116400538NAP1L3502590X9292848992928577

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample      1 1        
GAIN (# sample)      1 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)

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=148)
Stat. for Synonymous SNVs
(# total SNVs=44)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=2)

Top
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
chr12:116421304-116421304p.I1525V3
chr12:116424272-116424272p.P1379P2
chr12:116534502-116534502p.E151K2
chr12:116413011-116413011p.G1899V2
chr12:116445450-116445450p.?2
chr12:116429298-116429298p.N1154I2
chr12:116444160-116444160p.V765V2
chr12:116453082-116453083p.?2
chr12:116453083-116453083p.?2
chr12:116413354-116413354p.E1852Q2

Top
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
# sample332261 9 31 2097131915 24
# mutation332281 9 31 2497132022 40
nonsynonymous SNV332181 6 21 1956 11216 33
synonymous SNV   10  3 1  5411286 7
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])

Top
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
chr12:116457644p.S253S3
chr12:116413011p.G1957R2
chr12:116445418p.G1899V2
chr12:116457747p.R679L2
chr12:116421304p.T219M2
chr12:116444160p.R388K2
chr12:116409904p.V765V2
chr12:116452926p.I1525V2
chr12:116420250p.R1705H2
chr12:116457671p.A1977P1

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 MED13L 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]

Top
Gene Expression for MED13L

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

AFF4,ATXN2,BAZ2A,HECTD4,CREBRF,CLASP2,CPEB2,
CSNK1G3,DMXL1,FAM73A,HEATR5B,KIAA1109,KLHL11,LRBA,
MED13L,NEK4,RAD50,TBC1D12,TBC1D9,THSD4,ZFX
ASH1L,ATG2B,BIRC6,BOD1L1,CCNT1,CHD9,EP300,
HEATR5B,LATS1,MED13L,KMT2C,MYO9A,KAT6A,NF1,
NIPBL,SBNO1,SON,SP1,UBR5,USP34,ZKSCAN8

ASXL2,BIRC6,BOD1L1,HECTD4,CREBBP,EP300,EP400,
HERC1,HIPK3,HIVEP1,KIDINS220,MED13L,MKL2,KMT2B___KMT2D,
KMT2C,MYO9A,PLEKHM3,TAOK1,TRIO,TTBK2,USP34
ASH1L,ATXN1L,BOD1L1,HECTD4,CHD2,CREBBP,EP300,
GIGYF2,GON4L,GPATCH8,HELZ,MED13L,KMT2C,KMT2A,
KAT6A,KAT6B,NR2C2,POGZ,SMG6,TUG1,USP34
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for MED13L


There's no related Drug.
Top
Cross referenced IDs for MED13L
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas