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 CDK19

Basic gene info.	Gene symbol	CDK19
	Gene name	cyclin-dependent kinase 19
	Synonyms	CDC2L6\|CDK11\|bA346C16.3
	Cytomap	UCSC genome browser: 6q21
	Genomic location	chr6 :110931180-111136412
	Type of gene	protein-coding
	RefGenes	NM_001300960.1, NM_001300963.1,NM_001300964.1,NM_015076.4,
	Ensembl id	ENSG00000155111
	Description	CDC2-related protein kinase 6CDK8-like cyclin-dependent kinasecell division cycle 2-like 6 (CDK8-like)cell division cycle 2-like protein kinase 6cell division protein kinase 19cyclin dependent kinase 19 variant 2cyclin-dependent kinase (CDC2-like) 1
	Modification date	20141207
dbXrefs	MIM : 614720
	HGNC : HGNC
	Ensembl : ENSG00000155111
	HPRD : 07627
	Vega : OTTHUMG00000015365
Protein	UniProt: Q9BWU1 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CDK19
	BioGPS: 23097
	Gene Expression Atlas: ENSG00000155111
	The Human Protein Atlas: ENSG00000155111
Pathway	NCI Pathway Interaction Database: CDK19
	KEGG: CDK19
	REACTOME: CDK19
	ConsensusPathDB
	Pathway Commons: CDK19
Metabolism	MetaCyc: CDK19
	HUMANCyc: CDK19
Regulation	Ensembl's Regulation: ENSG00000155111
	miRBase: chr6 :110,931,180-111,136,412
	TargetScan: NM_001300960
	cisRED: ENSG00000155111
Context	iHOP: CDK19
	cancer metabolism search in PubMed: CDK19
	UCL Cancer Institute: CDK19
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CDK19 in cancer cell metabolism	1. Porter DC, Farmaki E, Altilia S, Schools GP, West DK, et al. (2012) Cyclin-dependent kinase 8 mediates chemotherapy-induced tumor-promoting paracrine activities. Proc Natl Acad Sci U S A 109: 13799-13804. doi: 10.1073/pnas.1206906109. pmid: 3427077 go to article

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Phenotypic Information for CDK19(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CDK19
	Familial Cancer Database: CDK19

* 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	614720; gene.
Orphanet
Disease	KEGG Disease: CDK19
	MedGen: CDK19 (Human Medical Genetics with Condition)
	ClinVar: CDK19
Phenotype	MGI: CDK19 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CDK19

Mutations for CDK19

* 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

There's no inter-chromosomal structural variation.

- 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
ovary	CDK19	chr6	111114389	111114409	CDK19	chr6	111114456	111114476
ovary	CDK19	chr6	111126644	111126664	PTPRK	chr6	128828628	128828648
pancreas	CDK19	chr6	110963953	110963973		chr6	110927596	110927616
pancreas	CDK19	chr6	111071010	111071030	CDK19	chr6	111071560	111071580
pancreas	CDK19	chr6	111133847	111133867		chr6	111265885	111265905

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 CDK19 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
AI244697	MNT	79	169	17	2292774	2292868	CDK19	169	215	6	111043645	111043990
BQ345738	OAF	1	283	11	120097557	120099714	CDK19	279	356	6	110942314	110942391
CD654079	CDK19	29	449	6	110975514	110975934	CDK19	443	638	6	110972244	110972440
AI207519	CDK19	15	244	6	110973947	110974176	USP14	241	694	18	211368	211820
BF591193	MNT	79	169	17	2292774	2292868	CDK19	169	215	6	111043645	111043990
CN411943	CDK19	1	64	6	110932410	110932473	CDK19	62	561	6	110931928	110932427

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=42)	Stat. for Synonymous SNVs (# total SNVs=13)

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
chr6:111136325-111136325	p.F5F	4
chr6:110991680-110991680	p.D90G	3
chr6:110935789-110935789	p.S486S	2
chr6:110935837-110935837	p.S470R	2
chr6:110942499-110942499	p.A395A	2
chr6:110944071-110944071	p.S326S	2
chr6:111136336-111136336	p.D2N	2
chr6:110944110-110944110	p.Q313H	2
chr6:110942566-110942566	p.Q373L	2
chr6:110948235-110948235	p.R254W	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	2	6		11			1		1			2	6	1		2	4	3		7
# mutation	2	6		9			1		1			3	6	1		2	4	3		8
nonsynonymous SNV		5		8			1		1			2	4	1		1	3	2		7
synonymous SNV	2	1		1								1	2			1	1	1		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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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
chr6:110991680	p.D90G	3
chr6:110935837	p.S470R	2
chr6:110948235	p.R112C	2
chr6:110988759	p.R254W	2
chr6:110935789	p.A347A	1
chr6:110959856	p.R200W	1
chr6:110943323	p.S486S	1
chr6:111136299	p.D344E	1
chr6:110948234	p.K170N	1
chr6:110959861	p.S326S	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 CDK19 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 CDK19

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


AK9,AMD1,ARMC2,CEP57L1,CD164,CD24,CDC40, CDK19,FOXO3,FOXO3B,HACE1,LHX1,MRGPRD,PRIM2, REV3L,RPF2,SEC63,SYNCRIP,TRAF3IP2,TUBE1,ZBTB24	ANKRD50,ARID2,BAZ2B,BRWD1,SUCO,C5orf42,MMS22L, CD2AP,CDK19,DPY19L3,ERBB2IP,MAP9,PPIP5K2,PUS7L, STAG2,SUZ12,TMEM194A,ZBTB41,ZFC3H1,ZMYM2,ZNF678

ARID1B,CDK19,CREBBP,DYNC1LI2,HECA,GLTSCR1L,KIAA0355, KIAA0430,KLHL24,LATS1,MED23,KMT2E,PHF3,PIK3CA, PLEKHM3,PTPRK,SCAF8,SERINC1,SOS1,TAB2,ZNF292	ATP9A,BAHD1,BTBD9,CDK19,COL17A1,CTDSP2,CXorf23, ERBB3,HECA,IGSF3,INSR,LOC90110,MKRN1,N4BP1, NBR1,PLCL2,RMND5A,RXRA,SLC26A2,SORL1,SPPL3

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 CDK19

There's no related Drug.

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Cross referenced IDs for CDK19

* 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