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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GALK1 |
Basic gene info. | Gene symbol | GALK1 |
Gene name | galactokinase 1 | |
Synonyms | GALK|GK1|HEL-S-19 | |
Cytomap | UCSC genome browser: 17q24 | |
Genomic location | chr17 :73754017-73761280 | |
Type of gene | protein-coding | |
RefGenes | NM_000154.1, | |
Ensembl id | ENSG00000108479 | |
Description | epididymis secretory protein Li 19galactokinasegalactose kinase | |
Modification date | 20141207 | |
dbXrefs | MIM : 604313 | |
HGNC : HGNC | ||
Ensembl : ENSG00000108479 | ||
HPRD : 05057 | ||
Vega : OTTHUMG00000179832 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GALK1 | |
BioGPS: 2584 | ||
Gene Expression Atlas: ENSG00000108479 | ||
The Human Protein Atlas: ENSG00000108479 | ||
Pathway | NCI Pathway Interaction Database: GALK1 | |
KEGG: GALK1 | ||
REACTOME: GALK1 | ||
ConsensusPathDB | ||
Pathway Commons: GALK1 | ||
Metabolism | MetaCyc: GALK1 | |
HUMANCyc: GALK1 | ||
Regulation | Ensembl's Regulation: ENSG00000108479 | |
miRBase: chr17 :73,754,017-73,761,280 | ||
TargetScan: NM_000154 | ||
cisRED: ENSG00000108479 | ||
Context | iHOP: GALK1 | |
cancer metabolism search in PubMed: GALK1 | ||
UCL Cancer Institute: GALK1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for GALK1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GALK1 |
Familial Cancer Database: GALK1 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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 | |
KEGG_GALACTOSE_METABOLISM KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GALK1 |
MedGen: GALK1 (Human Medical Genetics with Condition) | |
ClinVar: GALK1 | |
Phenotype | MGI: GALK1 (International Mouse Phenotyping Consortium) |
PhenomicDB: GALK1 |
Mutations for GALK1 |
* 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 | Top |
- 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 | GALK1 | chr17 | 73755472 | 73755492 | UNK | chr17 | 73781947 | 73781967 |
ovary | GALK1 | chr17 | 73755476 | 73755496 | UNK | chr17 | 73781947 | 73781967 |
ovary | GALK1 | chr17 | 73757377 | 73757397 | GRB2 | chr17 | 73373468 | 73373488 |
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 GALK1 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 |
Other DBs for Structural Variants |
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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 |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=11) | (# total SNVs=8) |
(# total SNVs=1) | (# total SNVs=0) |
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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 |
chr17:73754163-73754163 | p.D385Y | 2 |
chr17:73758813-73758813 | p.L255L | 2 |
chr17:73754661-73754661 | p.S271R | 1 |
chr17:73759238-73759238 | p.? | 1 |
chr17:73754672-73754672 | p.D268N | 1 |
chr17:73759465-73759465 | p.G137G | 1 |
chr17:73754172-73754172 | p.Q382E | 1 |
chr17:73759468-73759468 | p.G136G | 1 |
chr17:73754197-73754197 | p.G373G | 1 |
chr17:73758856-73758856 | p.R241H | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   | 3 | 1 |   |   |   |   |   |   | 1 |   |   |   |   | 4 | 3 |   | 3 |
# mutation | 2 |   |   | 2 | 1 |   |   |   |   |   |   | 1 |   |   |   |   | 3 | 3 |   | 3 |
nonsynonymous SNV | 1 |   |   | 1 | 1 |   |   |   |   |   |   | 1 |   |   |   |   | 1 | 2 |   | 1 |
synonymous SNV | 1 |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   | 2 | 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 |
chr17:73760039 | p.L255L | 2 |
chr17:73758813 | p.S98S | 2 |
chr17:73759118 | p.D385Y | 1 |
chr17:73754163 | p.T344T | 1 |
chr17:73759154 | p.T288T | 1 |
chr17:73754366 | p.S271R | 1 |
chr17:73759198 | p.D268N | 1 |
chr17:73754610 | p.R241H | 1 |
chr17:73754661 | p.S234G | 1 |
chr17:73761135 | p.I222M | 1 |
Other DBs for Point Mutations |
Copy Number for GALK1 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 GALK1 |
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. |
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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 |
ANAPC11,ASPSCR1,TEN1,OXLD1,C19orf60,FAM207A,CCDC124, CCDC137,CHMP6,CLPP,FAM195B,FAM50A,GALK1,JMJD6, MAD1L1,MRPL12,MRPL38,NT5C,RFNG,SAP30BP,TSEN54 | ALDH16A1,ASPSCR1,COPE,CRELD2,CYBA,DPP7,MVB12A, FBXL15,GALK1,GNB2,MBD3,MPG,PSMB10,PTRH1, RBM42,SIRT6,SNAPC2,SSBP4,TBCB,TRMT61A,ZNF668 | ||||
ANAPC11,TEN1,TMEM256,PTRHD1,COPE,MZT2B,GALK1, GEMIN7,ILVBL,MIF,MRPL12,MRPL27,MRPL38,MRPS12, MRPS7,PRMT1,SF3B5,SIVA1,SMPD2,YIF1A,YIF1B | AQP3,SLC25A47,CD82,CRIP1,DNASE1,EMB,F11, GALK1,GALNT14,GCHFR,KCP,LOC647121,MS4A15,PFKFB4, PLB1,RBP3,SAT2,SEC14L2,SERPINA1,TMEM92,VNN1 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for GALK1 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
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 |
DB03431 | galactokinase 1 | experimental | Adenosine-5'-Diphosphate | ||
DB04395 | galactokinase 1 | experimental | Phosphoaminophosphonic Acid-Adenylate Ester |
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Cross referenced IDs for GALK1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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