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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GLYCTK |
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Phenotypic Information for GLYCTK(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: GLYCTK |
Familial Cancer Database: GLYCTK |
* This gene is included in those cancer gene databases. |
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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/ |
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KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM KEGG_GLYCEROLIPID_METABOLISM KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: GLYCTK |
MedGen: GLYCTK (Human Medical Genetics with Condition) | |
ClinVar: GLYCTK | |
Phenotype | MGI: GLYCTK (International Mouse Phenotyping Consortium) |
PhenomicDB: GLYCTK |
Mutations for GLYCTK |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GLYCTK 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 |
BU752122 | GLYCTK | 17 | 92 | 3 | 52327412 | 52327487 | PSG3 | 88 | 148 | 19 | 43262184 | 43262244 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=24) | (# total SNVs=8) |
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(# total SNVs=1) | (# total SNVs=0) |
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* 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 |
chr3:52326621-52326621 | p.L351V | 2 |
chr3:52326290-52326290 | p.I240I | 2 |
chr3:52325015-52325015 | p.F139F | 2 |
chr3:52326932-52326932 | p.Q454H | 2 |
chr3:52324415-52324415 | p.L19L | 2 |
chr3:52325039-52325039 | p.P147P | 2 |
chr3:52324538-52324538 | p.S60S | 2 |
chr3:52324642-52324642 | p.A95G | 1 |
chr3:52326848-52326848 | p.L426L | 1 |
chr3:52325769-52325769 | p.G179fs*34 | 1 |
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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 | 3 | 2 |   | 2 |   |   | 1 |   | 1 |   |   | 4 |   |   |   |   | 8 | 5 | 1 | 5 |
# mutation | 3 | 2 |   | 2 |   |   | 1 |   | 1 |   |   | 4 |   |   |   |   | 7 | 5 | 1 | 5 |
nonsynonymous SNV | 3 | 2 |   | 2 |   |   | 1 |   | 1 |   |   | 2 |   |   |   |   | 1 | 3 |   | 2 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   | 2 |   |   |   |   | 6 | 2 | 1 | 3 |
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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* 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 |
chr3:52325015 | p.L19L,GLYCTK | 2 |
chr3:52324415 | p.S60S,GLYCTK | 2 |
chr3:52324538 | p.F139F,GLYCTK | 2 |
chr3:52325000 | p.R153W,GLYCTK | 1 |
chr3:52326415 | p.P438P | 1 |
chr3:52327124 | p.I158I,GLYCTK | 1 |
chr3:52326603 | p.S448S | 1 |
chr3:52325046 | p.L182V | 1 |
chr3:52326740 | p.V512V | 1 |
chr3:52325055 | p.R205C | 1 |
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* 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. |
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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 GLYCTK |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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C16orf86,TMEM259,C21orf2,CAMK1,CAPN10,CCDC88B,EXOC3L1, FBXL15,GLYCTK,GRASP,IFFO1,KANK3,LYL1,MBD3, NDUFS7,PPP1R12C,SCRN2,SELO,SNRNP70,TNFRSF14,USHBP1 | ACSM2A,ACSM2B,AMN,APOC3,APOL4,ASS1,BMP3, TBATA,IZUMO4,CALCRL,GLUL,GLYCTK,LOC100101938,MOGAT1, NDRG4,NTSR2,PDZD7,PMM1,RASL10B,SNORA14A,ST8SIA3 |
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ABCC6P1,ACOT11,ACY1,SMIM24,RBBP8NL,CYB561D2,CYP2D6, DAK,DDC,GLYCTK,HDHD3,HEMK1,IFRD2,METTL7B, MYO1A,OGFOD2,SLC51B,PMM2,SLC39A5,TUBAL3,TUSC2 | ACY1,AKR7A3,AKR7L,SOWAHA,CDHR5,CYP2B6,CYP2C18, CYP4F12,DAPK2,GDA,SLX1B,GLYCTK,INPP5J,MYO1A, PCK2,PDXP,PRAP1,RBKS,SLC23A3,SLC39A5,TMEM120A |
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* 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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Pharmacological Information for GLYCTK |
There's no related Drug. |
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Cross referenced IDs for GLYCTK |
* 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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