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 symbolCDK19
Gene namecyclin-dependent kinase 19
SynonymsCDC2L6|CDK11|bA346C16.3
CytomapUCSC genome browser: 6q21
Genomic locationchr6 :110931180-111136412
Type of geneprotein-coding
RefGenesNM_001300960.1,
NM_001300963.1,NM_001300964.1,NM_015076.4,
Ensembl idENSG00000155111
DescriptionCDC2-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 date20141207
dbXrefs MIM : 614720
HGNC : HGNC
Ensembl : ENSG00000155111
HPRD : 07627
Vega : OTTHUMG00000015365
ProteinUniProt: Q9BWU1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CDK19
BioGPS: 23097
Gene Expression Atlas: ENSG00000155111
The Human Protein Atlas: ENSG00000155111
PathwayNCI Pathway Interaction Database: CDK19
KEGG: CDK19
REACTOME: CDK19
ConsensusPathDB
Pathway Commons: CDK19
MetabolismMetaCyc: CDK19
HUMANCyc: CDK19
RegulationEnsembl's Regulation: ENSG00000155111
miRBase: chr6 :110,931,180-111,136,412
TargetScan: NM_001300960
cisRED: ENSG00000155111
ContextiHOP: CDK19
cancer metabolism search in PubMed: CDK19
UCL Cancer Institute: CDK19
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CDK19 in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 614720; gene.
Orphanet
DiseaseKEGG Disease: CDK19
MedGen: CDK19 (Human Medical Genetics with Condition)
ClinVar: CDK19
PhenotypeMGI: CDK19 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryCDK19chr6111114389111114409CDK19chr6111114456111114476
ovaryCDK19chr6111126644111126664PTPRKchr6128828628128828648
pancreasCDK19chr6110963953110963973chr6110927596110927616
pancreasCDK19chr6111071010111071030CDK19chr6111071560111071580
pancreasCDK19chr6111133847111133867chr6111265885111265905
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 CDK19 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI244697MNT791691722927742292868CDK191692156111043645111043990
BQ345738OAF128311120097557120099714CDK192793566110942314110942391
CD654079CDK19294496110975514110975934CDK194436386110972244110972440
AI207519CDK19152446110973947110974176USP1424169418211368211820
BF591193MNT791691722927742292868CDK191692156111043645111043990
CN411943CDK191646110932410110932473CDK19625616110931928110932427

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2  1    1 3      
GAIN (# sample)2  1      2      
LOSS (# sample)        1 1      
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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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

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check002.gifSomatic 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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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
chr6:111136325-111136325p.F5F4
chr6:110991680-110991680p.D90G3
chr6:110948235-110948235p.R254W2
chr6:110935789-110935789p.S486S2
chr6:110935837-110935837p.S470R2
chr6:110942499-110942499p.A395A2
chr6:110944071-110944071p.S326S2
chr6:111136336-111136336p.D2N2
chr6:110944110-110944110p.Q313H2
chr6:110942566-110942566p.Q373L2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample26 11  1 1  261 243 7
# mutation26 9  1 1  361 243 8
nonsynonymous SNV 5 8  1 1  241 132 7
synonymous SNV21 1       12  111 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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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
chr6:110991680p.D90G3
chr6:110935837p.S470R2
chr6:110948235p.R112C2
chr6:110988759p.R254W2
chr6:110944115p.G348C1
chr6:110953250p.G207V1
chr6:110942423p.A347A1
chr6:110944513p.R200W1
chr6:110953259p.S486S1
chr6:111067348p.D344E1

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 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

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

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
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 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



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