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 GALK2
Basic gene info.Gene symbolGALK2
Gene namegalactokinase 2
SynonymsGK2
CytomapUCSC genome browser: 15q21.1-q21.2
Genomic locationchr15 :49447975-49622002
Type of geneprotein-coding
RefGenesNM_001001556.2,
NM_001289030.1,NM_001289031.1,NM_002044.3,
Ensembl idENSG00000156958
DescriptionN-acetylgalactosamine kinasegalNAc kinase
Modification date20141207
dbXrefs MIM : 137028
HGNC : HGNC
HPRD : 00657
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALK2
BioGPS: 2585
Gene Expression Atlas: ENSG00000156958
The Human Protein Atlas: ENSG00000156958
PathwayNCI Pathway Interaction Database: GALK2
KEGG: GALK2
REACTOME: GALK2
ConsensusPathDB
Pathway Commons: GALK2
MetabolismMetaCyc: GALK2
HUMANCyc: GALK2
RegulationEnsembl's Regulation: ENSG00000156958
miRBase: chr15 :49,447,975-49,622,002
TargetScan: NM_001001556
cisRED: ENSG00000156958
ContextiHOP: GALK2
cancer metabolism search in PubMed: GALK2
UCL Cancer Institute: GALK2
Assigned class in ccmGDBC

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Phenotypic Information for GALK2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALK2
Familial Cancer Database: GALK2
* 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
KEGG_GALACTOSE_METABOLISM
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GALK2
MedGen: GALK2 (Human Medical Genetics with Condition)
ClinVar: GALK2
PhenotypeMGI: GALK2 (International Mouse Phenotyping Consortium)
PhenomicDB: GALK2

Mutations for GALK2
* 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
liverGALK2chr154960690449606904C15orf33chr154968064749680647
liverGALK2chr154960691149606911C15orf33chr154968062849680628
ovaryGALK2chr154959838449598404GALK2chr154952263349522653
pancreasGALK2chr154961423649614256GALK2chr154957362349573643
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 GALK2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB216138GALK21319154944799549454059GOPC3175466117896453117900229
BF355333PDIA37194154405909044061776GALK2181255154959933749599411

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)1               1
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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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=39)
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
chr15:49620186-49620186p.G392*3
chr15:49531550-49531550p.R153W2
chr15:49509510-49509510p.P78L2
chr15:49528110-49528110p.Y99C2
chr15:49584622-49584622p.V274V2
chr15:49493420-49493420p.R28*2
chr15:49575800-49575800p.D203V2
chr15:49620214-49620214p.V401G1
chr15:49575902-49575902p.R237Q1
chr15:49509474-49509474p.Y66F1

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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
# sample 1 81 1 1  52   22 5
# mutation 1 81 1 1  52   22 5
nonsynonymous SNV 1 51 1 1  31   22 3
synonymous SNV   3       21      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
chr15:49584700p.A186A,GALK21
chr15:49531528p.T435S,GALK21
chr15:49584724p.P207P,GALK21
chr15:49531560p.R237Q,GALK21
chr15:49584728p.L238M,GALK21
chr15:49574198p.D252G,GALK21
chr15:49611853p.N16S,GALK21
chr15:49493385p.L279F,GALK21
chr15:49574270p.G20G,GALK21
chr15:49611861p.E282V,GALK21

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 GALK2 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 GALK2

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

ALDH1A2,AP4E1,ARPP19,FAM227B,COPS2,CYP2C9,DTWD1,
DUT,FLJ10038,GALK2,HAUS2,HK1,LOC100129387,LRRC57,
PIGB,BLOC1S6,RSL24D1,SPANXD,SPATA5L1,SUPV3L1,VPS26A
ABCB6,AUH,C10orf76,CCBL1,CRADD,FDFT1,GALK2,
HIBCH,HIST1H1D,KLHL8,LOC81691,NGLY1,NUDT9,OMA1,
RIC8B,SCP2,SRBD1,STAMBP,TBCK,UTP6,YARS2

AQR,VWA9,RHOV___CHP1,CKMT1B,CLN6,CLPX,COPS2,
COX15,COX5A,ETFA,GALK2,IVD,LEO1,MPI,
NDUFAF1,RAB11A,RPP25,RPUSD2,SFXN2,SLC27A2,SPATA5L1
AK7,AURKA,CCNB1,CCNB2,CENPN,CHCHD3,COQ2,
DIAPH3,MTFR2,FH,GALK2,GMDS,MELK,NCAPG,
OIP5,ORC1,PBK,POC1A,RAD51,RARS,RTN4IP1
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 GALK2


There's no related Drug.
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Cross referenced IDs for GALK2
* 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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