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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GCNT4 |
Basic gene info. | Gene symbol | GCNT4 |
Gene name | glucosaminyl (N-acetyl) transferase 4, core 2 | |
Synonyms | C2GNT3 | |
Cytomap | UCSC genome browser: 5q12 | |
Genomic location | chr5 :74323288-74326724 | |
Type of gene | protein-coding | |
RefGenes | NM_016591.2, | |
Ensembl id | ENSG00000176928 | |
Description | beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4core 2 beta-1,6-N-acetylglucosaminyltransferase 3core 2-branching enzyme 3core2-GlcNAc-transferase 3glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylg | |
Modification date | 20141207 | |
dbXrefs | HGNC : HGNC | |
HPRD : 16651 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GCNT4 | |
BioGPS: 51301 | ||
Gene Expression Atlas: ENSG00000176928 | ||
The Human Protein Atlas: ENSG00000176928 | ||
Pathway | NCI Pathway Interaction Database: GCNT4 | |
KEGG: GCNT4 | ||
REACTOME: GCNT4 | ||
ConsensusPathDB | ||
Pathway Commons: GCNT4 | ||
Metabolism | MetaCyc: GCNT4 | |
HUMANCyc: GCNT4 | ||
Regulation | Ensembl's Regulation: ENSG00000176928 | |
miRBase: chr5 :74,323,288-74,326,724 | ||
TargetScan: NM_016591 | ||
cisRED: ENSG00000176928 | ||
Context | iHOP: GCNT4 | |
cancer metabolism search in PubMed: GCNT4 | ||
UCL Cancer Institute: GCNT4 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for GCNT4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GCNT4 |
Familial Cancer Database: GCNT4 |
* 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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GCNT4 |
MedGen: GCNT4 (Human Medical Genetics with Condition) | |
ClinVar: GCNT4 | |
Phenotype | MGI: GCNT4 (International Mouse Phenotyping Consortium) |
PhenomicDB: GCNT4 |
Mutations for GCNT4 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GCNT4 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=38) | (# total SNVs=7) |
(# total SNVs=3) | (# total SNVs=1) |
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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 |
chr5:74324548-74324548 | p.P439S | 4 |
chr5:74324606-74324606 | p.I419I | 3 |
chr5:74324902-74324902 | p.V321I | 3 |
chr5:74325746-74325746 | p.P39P | 2 |
chr5:74325583-74325583 | p.D94Y | 2 |
chr5:74324983-74324983 | p.H294fs*14 | 2 |
chr5:74325720-74325720 | p.Y48C | 2 |
chr5:74324763-74324763 | p.R367H | 1 |
chr5:74325002-74325002 | p.I287I | 1 |
chr5:74324587-74324587 | p.E426Q | 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 | 2 |   | 9 | 1 |   | 2 |   | 1 | 1 |   | 8 |   | 4 |   |   | 3 | 4 |   | 4 |
# mutation | 2 | 2 |   | 11 | 1 |   | 2 |   | 1 | 1 |   | 8 |   | 4 |   |   | 4 | 4 |   | 4 |
nonsynonymous SNV | 2 | 2 |   | 10 | 1 |   | 2 |   | 1 | 1 |   | 5 |   | 4 |   |   | 3 | 2 |   | 1 |
synonymous SNV |   |   |   | 1 |   |   |   |   |   |   |   | 3 |   |   |   |   | 1 | 2 |   | 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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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 |
chr5:74325583 | p.D94Y | 2 |
chr5:74324606 | p.I419I | 2 |
chr5:74324903 | p.E83V | 1 |
chr5:74325216 | p.R399S | 1 |
chr5:74324666 | p.H269Y | 1 |
chr5:74325615 | p.E78A | 1 |
chr5:74324987 | p.R399G | 1 |
chr5:74325251 | p.F265L | 1 |
chr5:74324668 | p.S74S | 1 |
chr5:74325630 | p.G394E | 1 |
Other DBs for Point Mutations |
Copy Number for GCNT4 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 GCNT4 |
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 |
AFF3,ANKRD29,HNF1A-AS1,C12orf42,C2orf50,CDK17,CPEB4, DMXL1,FAM169A,FBXO38,GCNT4,LAMA3,LOC144742,MAGI1, NPTX1,OR5B2,RP1,S1PR3,SRRM4,SYTL4,TRIM23 | ARHGAP5,ASCC3,BBX,PCNXL4,CCP110,GCNT4,GOPC, GLTSCR1L,KIAA2026,KLHL42,MRE11A,NPAT,PGAP1,PURB, RBMXL1,RTTN,U2SURP,VPS36,WDR35,ZNF121,ZNF638 |
ACER2,BCAS1,CCNG2,CD3G,CD40LG,CFD,CRYBB1, EVI2B,GCNT4,HCFC2,KAT2B,KLRB1,PLCL2,RAB27A, SLCO2A1,STK17B,SWAP70,TBC1D10A,THEMIS,TRANK1,VSIG2 | APOA5,SMIM24,C1orf105,TMEM252,CYP4A11,DAB1,DHDH, FADS6,G6PC,GCNT4,HOXC8,HSD3B1,MS4A10,NAALADL1, NAT8,NAT8B,NLRP6,SLC15A1,SLC6A4,TMEM229A,UGT1A4 |
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 GCNT4 |
There's no related Drug. |
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Cross referenced IDs for GCNT4 |
* 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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