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 CSNK1G2
Basic gene info.Gene symbolCSNK1G2
Gene namecasein kinase 1, gamma 2
SynonymsCK1g2
CytomapUCSC genome browser: 19p13.3
Genomic locationchr19 :1941160-1981336
Type of geneprotein-coding
RefGenesNM_001319.6,
Ensembl idENSG00000133275
DescriptionCKI-gamma 2casein kinase 1 isoform gamma-2casein kinase I isoform gamma-2
Modification date20141207
dbXrefs MIM : 602214
HGNC : HGNC
Ensembl : ENSG00000133275
HPRD : 03738
Vega : OTTHUMG00000180016
ProteinUniProt: P78368
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CSNK1G2
BioGPS: 1455
Gene Expression Atlas: ENSG00000133275
The Human Protein Atlas: ENSG00000133275
PathwayNCI Pathway Interaction Database: CSNK1G2
KEGG: CSNK1G2
REACTOME: CSNK1G2
ConsensusPathDB
Pathway Commons: CSNK1G2
MetabolismMetaCyc: CSNK1G2
HUMANCyc: CSNK1G2
RegulationEnsembl's Regulation: ENSG00000133275
miRBase: chr19 :1,941,160-1,981,336
TargetScan: NM_001319
cisRED: ENSG00000133275
ContextiHOP: CSNK1G2
cancer metabolism search in PubMed: CSNK1G2
UCL Cancer Institute: CSNK1G2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CSNK1G2 in cancer cell metabolism1. Mishra SK, Yang Z, Mazumdar A, Talukder AH, Larose L, et al. (2004) Metastatic tumor antigen 1 short form (MTA1s) associates with casein kinase I-gamma2, an estrogen-responsive kinase. Oncogene 23: 4422-4429. doi: 10.1038/sj.onc.1207569. go to article
2. Guo X, Waddell DS, Wang W, Wang Z, Liberati NT, et al. (2008) Ligand-dependent ubiquitination of Smad3 is regulated by casein kinase 1 gamma 2, an inhibitor of TGF-beta signaling. Oncogene 27: 7235-7247. doi: 10.1038/onc.2008.337. pmid: 2643063. go to article

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Phenotypic Information for CSNK1G2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CSNK1G2
Familial Cancer Database: CSNK1G2
* 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_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 602214; gene.
Orphanet
DiseaseKEGG Disease: CSNK1G2
MedGen: CSNK1G2 (Human Medical Genetics with Condition)
ClinVar: CSNK1G2
PhenotypeMGI: CSNK1G2 (International Mouse Phenotyping Consortium)
PhenomicDB: CSNK1G2

Mutations for CSNK1G2
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 CSNK1G2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI040601MAST23722114649136946493468CSNK1G22195061919789961979513
BF064078CSNK1G212611919802071980467CSNK1G22564051919806821980831
BQ331903CSNK1G2122951919695281969813NBPF112883111147778120147778145

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 # sample1     1          
GAIN (# sample)                 
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=21)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr19:1979040-1979040p.K210K2
chr19:1978869-1978869p.M153I2
chr19:1979336-1979336p.R263W2
chr19:1969835-1969835p.G22C2
chr19:1979386-1979386p.L279L2
chr19:1979502-1979502p.A288T2
chr19:1978706-1978706p.R135L2
chr19:1969891-1969891p.L40L2
chr19:1969905-1969905p.N45S1
chr19:1979550-1979550p.D304N1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample3  3       2    23 4
# mutation3  3       2    25 4
nonsynonymous SNV           1    15 2
synonymous SNV3  3       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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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
chr19:1978308p.I204T1
chr19:1979046p.P205L1
chr19:1978449p.L212L1
chr19:1979366p.A273T1
chr19:1978629p.G22C1
chr19:1979526p.R296C1
chr19:1978632p.R31W1
chr19:1979554p.Y305C1
chr19:1978657p.L40L1
chr19:1979753p.P335P1

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 CSNK1G2 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 CSNK1G2

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

ADAT3,APBA3,BTBD2,CACTIN,TMEM259,CSNK1G2,DAZAP1,
DOHH,ABHD17A,KLF16,MBD3,MIB2,MIER2,NCLN,
PLEKHJ1,POLRMT,REXO1,RNF126,SBNO2,SPPL2B,STK11
ATAD3A,AXIN1,CEP131,CACTIN,CC2D1A,CSNK1G2,CTDP1,
DDX54,LRRC45,LRWD1,MAP1S,PNKP,RABEP2,RHOT2,
SCAF1,SCRIB,CAPN15,TELO2,TRABD,U2AF2,ZNF598

AP3D1,CACTIN,TMEM259,CSNK1G2,DOHH,DOT1L,DPP9,
ELL,FZR1,LMNB2,MLLT1,PIAS4,POLRMT,RANBP3,
RAVER1,REXO1,SGTA,SMARCA4,STK11,TCF3,UPF1
TMEM259,CCDC88B,CELSR3,CORO7,CSNK1G2,EHMT1,EML3,
FBXL19,GRIPAP1,MCM3AP,MYO9B,P2RY11,PIGQ,RNF31,
SBF1,SCAMP4,SCRIB,TRABD,TYK2,ZC3H3,ZNF598
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 CSNK1G2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P78368; -.
ChemistryChEMBL CHEMBL2111458; -.
ChemistryGuidetoPHARMACOLOGY 2000; -.
Organism-specific databasesPharmGKB PA26955; -.
Organism-specific databasesCTD 1455; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB03083casein kinase 1, gamma 2experimentalIC261
DB03693casein kinase 1, gamma 2experimentalN-(2-Aminoethyl)-5-Chloroisoquinoline-8-Sulfonamide
DB04604casein kinase 1, gamma 2experimental5-iodotubercidin


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Cross referenced IDs for CSNK1G2
* 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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