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 MAPK11

Basic gene info.	Gene symbol	MAPK11
	Gene name	mitogen-activated protein kinase 11
	Synonyms	P38B\|P38BETA2\|PRKM11\|SAPK2\|SAPK2B\|p38-2\|p38Beta
	Cytomap	UCSC genome browser: 22q13.33
	Genomic location	chr22 :50702141-50708779
	Type of gene	protein-coding
	RefGenes	NM_002751.6, NR_110887.1,
	Ensembl id	ENSG00000185386
	Description	MAP kinase 11MAP kinase p38 betamitogen-activated protein kinase p38 betamitogen-activated protein kinase p38-2stress-activated protein kinase-2stress-activated protein kinase-2b
	Modification date	20141222
dbXrefs	MIM : 602898
	HGNC : HGNC
	Ensembl : ENSG00000185386
	HPRD : 04208
	Vega : OTTHUMG00000150226
Protein	UniProt: Q15759 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MAPK11
	BioGPS: 5600
	Gene Expression Atlas: ENSG00000185386
	The Human Protein Atlas: ENSG00000185386
Pathway	NCI Pathway Interaction Database: MAPK11
	KEGG: MAPK11
	REACTOME: MAPK11
	ConsensusPathDB
	Pathway Commons: MAPK11
Metabolism	MetaCyc: MAPK11
	HUMANCyc: MAPK11
Regulation	Ensembl's Regulation: ENSG00000185386
	miRBase: chr22 :50,702,141-50,708,779
	TargetScan: NM_002751
	cisRED: ENSG00000185386
Context	iHOP: MAPK11
	cancer metabolism search in PubMed: MAPK11
	UCL Cancer Institute: MAPK11
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for MAPK11(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MAPK11
	Familial Cancer Database: MAPK11

* 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_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	602898; gene. 602898; gene.
Orphanet
Disease	KEGG Disease: MAPK11
	MedGen: MAPK11 (Human Medical Genetics with Condition)
	ClinVar: MAPK11
Phenotype	MGI: MAPK11 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MAPK11

Mutations for MAPK11

* 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

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MAPK11 related fusion information.

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

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

There's no copy number variation information in COSMIC data for this gene.

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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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=19)	Stat. for Synonymous SNVs (# total SNVs=5)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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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
chr22:50705712-50705712	p.I141L	2
chr22:50703850-50703850	p.H305H	2
chr22:50704661-50704661	p.S252S	1
chr22:50705436-50705436	p.M179I	1
chr22:50708690-50708690	p.Q11fs*3	1
chr22:50704662-50704662	p.S252*	1
chr22:50705455-50705455	p.R173L	1
chr22:50704717-50704717	p.R234C	1
chr22:50705474-50705474	p.L167M	1
chr22:50704973-50704973	p.S226S	1

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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=2

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	2		1		1		3					1	1				2	1		4
# mutation	2		1		1		3					1	1				2	1		5
nonsynonymous SNV	2		1		1		2					1	1				1	1		3
synonymous SNV							1										1			2

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
chr22:50703900	p.L289V	2
chr22:50704989	p.R173L	1
chr22:50705394	p.L167M	1
chr22:50705416	p.R149W	1
chr22:50705436	p.E125K	1
chr22:50705455	p.I116N	1
chr22:50703752	p.V52M	1
chr22:50705474	p.K338R	1
chr22:50703786	p.V327I	1
chr22:50705688	p.H305H	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 MAPK11 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 MAPK11

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


CCM2,CLDN5,COX4I2,EXOC3L1,ABHD17A,GLYCTK,GRASP, HDAC10,KANK3,LMF2,LYL1,MAPK11,MAPK12,PLAC9, INAFM1,RNF166,RPS19BP1,SELO,TNFRSF4,TWF2,VAMP5	AGPAT2,ASS1,C20orf27,CAMK1,CKB,EFNB1,FCN3, FPGS,GCHFR,KANK3,MAPK11,MPST,PC,PHLDA3, PMM1,POLR2E,PQLC1,SLC25A1,SLC2A4RG,TMEM120A,UBTD1

ADARB1,CCM2L,CCDC88A,EVL,FAM167B,NXPE3,GIMAP1, GIMAP4,HAPLN3,HSPA12B,KANK3,LYL1,MAPK11,NFATC1, PEAR1,PIK3CD,SH2D3C,TSPAN4,VEGFC,ZBTB46,ZNF467	ARHGEF15,C1R,C1S,CDH5,CLU,DCLK1,DOC2B, GJA4,GPR173,HSPA12B,MAPK11,MMP2,PCDH17,PECAM1, PRRX1,ROBO4,SERPING1,THSD1,THY1,TIE1,TIMP1

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 MAPK11

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q15759; -.
Chemistry	ChEMBL	CHEMBL3961; -.
Chemistry	GuidetoPHARMACOLOGY	1500; -.
Chemistry	BindingDB	Q15759; -.
Chemistry	ChEMBL	CHEMBL3961; -.
Chemistry	GuidetoPHARMACOLOGY	1500; -.
Organism-specific databases	PharmGKB	PA30618; -.
Organism-specific databases	PharmGKB	PA30618; -.
Organism-specific databases	CTD	5600; -.
Organism-specific databases	CTD	5600; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01234	mitogen-activated protein kinase 11	approved; investigational	Dexamethasone
DB00398	mitogen-activated protein kinase 11	approved; investigational	Sorafenib
DB00435	mitogen-activated protein kinase 11	approved	Nitric Oxide
DB00125	mitogen-activated protein kinase 11	approved; nutraceutical	L-Arginine

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Cross referenced IDs for MAPK11

* 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