Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 MED13L

Basic gene info.	Gene symbol	MED13L
	Gene name	mediator complex subunit 13-like
	Synonyms	PROSIT240\|THRAP2\|TRAP240L
	Cytomap	UCSC genome browser: 12q24.21
	Genomic location	chr12 :116396380-116714991
	Type of gene	protein-coding
	RefGenes	NM_015335.4,
	Ensembl id	ENSG00000123066
	Description	mediator of RNA polymerase II transcription subunit 13-likethyroid hormone receptor-associated protein 2thyroid hormone receptor-associated protein complex 240 kDa component-like
	Modification date	20141207
dbXrefs	MIM : 608771
	HGNC : HGNC
	HPRD : 10579
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MED13L
	BioGPS: 23389
	Gene Expression Atlas: ENSG00000123066
	The Human Protein Atlas: ENSG00000123066
Pathway	NCI Pathway Interaction Database: MED13L
	KEGG: MED13L
	REACTOME: MED13L
	ConsensusPathDB
	Pathway Commons: MED13L
Metabolism	MetaCyc: MED13L
	HUMANCyc: MED13L
Regulation	Ensembl's Regulation: ENSG00000123066
	miRBase: chr12 :116,396,380-116,714,991
	TargetScan: NM_015335
	cisRED: ENSG00000123066
Context	iHOP: MED13L
	cancer metabolism search in PubMed: MED13L
	UCL Cancer Institute: MED13L
Assigned class in ccmGDB	C

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Phenotypic Information for MED13L(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: MED13L
	MedGen: MED13L (Human Medical Genetics with Condition)
	ClinVar: MED13L
Phenotype	MGI: MED13L (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	MED13L	chr12	116451691	116451691	MED13L	chr12	116476980	116476980
ovary	MED13L	chr12	116401464	116401484		chr22	37647327	37647347
ovary	MED13L	chr12	116427802	116427822		chr12	113947591	113947611
ovary	MED13L	chr12	116564989	116565009	MED13L	chr12	116565502	116565522

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MED13L related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
CK824480	MED13L	33	140	12	116558166	116558273	SERPINI2	136	522	3	167173569	167173955
BF934070	MED13L	13	250	12	116595421	116595660	MAP1B	247	498	5	71504071	71504322
BF357082	MED13L	1	265	12	116666969	116667232	PTPN23	260	279	3	47439467	47439486
AW809452	HEATR2	161	434	7	776821	777229	MED13L	431	569	12	116578385	116578523
AA502152	MED13L	1	123	12	116441537	116441659	MED13L	115	312	12	116441733	116441930
CK824479	SERPINI2	1	516	3	167173440	167173955	MED13L	512	586	12	116558166	116558240
BG988299	MED13L	1	65	12	116403886	116403951	GTPBP4	55	304	10	1056410	1058602
DA392149	MED13L	1	501	12	116398992	116400538	NAP1L3	502	590	X	92928489	92928577

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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

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Somatic 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)

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Top 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 position	Mutation(aa)	Unique sampleID count
chr12:116421304-116421304	p.I1525V	3
chr12:116424272-116424272	p.P1379P	2
chr12:116534502-116534502	p.E151K	2
chr12:116413011-116413011	p.G1899V	2
chr12:116445450-116445450	p.?	2
chr12:116429298-116429298	p.N1154I	2
chr12:116444160-116444160	p.V765V	2
chr12:116453082-116453083	p.?	2
chr12:116453083-116453083	p.?	2
chr12:116413354-116413354	p.E1852Q	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	3	3	2	26	1		9		3	1		20	9	7	1	3	19	15		24
# mutation	3	3	2	28	1		9		3	1		24	9	7	1	3	20	22		40
nonsynonymous SNV	3	3	2	18	1		6		2	1		19	5	6		1	12	16		33
synonymous SNV				10			3		1			5	4	1	1	2	8	6		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])

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Top 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 Position	Mutation(aa)	Unique sampleID count
chr12:116457644	p.S253S	3
chr12:116413011	p.G1957R	2
chr12:116445418	p.G1899V	2
chr12:116457747	p.R679L	2
chr12:116421304	p.T219M	2
chr12:116444160	p.R388K	2
chr12:116409904	p.V765V	2
chr12:116452926	p.I1525V	2
chr12:116420250	p.R1705H	2
chr12:116457671	p.A1977P	1

Other 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

Copy 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]

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Gene Expression for MED13L

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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 MED13L

There's no related Drug.

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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