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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GALNT1 |
Basic gene info. | Gene symbol | GALNT1 |
Gene name | polypeptide N-acetylgalactosaminyltransferase 1 | |
Synonyms | GALNAC-T1 | |
Cytomap | UCSC genome browser: 18q12.1 | |
Genomic location | chr18 :33234532-33291798 | |
Type of gene | protein-coding | |
RefGenes | NM_020474.3, | |
Ensembl id | ENSG00000141429 | |
Description | GalNAc transferase 1UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1)polypeptide GalNAc transferase 1pp-GaNTase 1protein-UDP acetylgalactosaminyltr | |
Modification date | 20141207 | |
dbXrefs | MIM : 602273 | |
HGNC : HGNC | ||
Ensembl : ENSG00000141429 | ||
HPRD : 03781 | ||
Vega : OTTHUMG00000132567 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GALNT1 | |
BioGPS: 2589 | ||
Gene Expression Atlas: ENSG00000141429 | ||
The Human Protein Atlas: ENSG00000141429 | ||
Pathway | NCI Pathway Interaction Database: GALNT1 | |
KEGG: GALNT1 | ||
REACTOME: GALNT1 | ||
ConsensusPathDB | ||
Pathway Commons: GALNT1 | ||
Metabolism | MetaCyc: GALNT1 | |
HUMANCyc: GALNT1 | ||
Regulation | Ensembl's Regulation: ENSG00000141429 | |
miRBase: chr18 :33,234,532-33,291,798 | ||
TargetScan: NM_020474 | ||
cisRED: ENSG00000141429 | ||
Context | iHOP: GALNT1 | |
cancer metabolism search in PubMed: GALNT1 | ||
UCL Cancer Institute: GALNT1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for GALNT1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GALNT1 |
Familial Cancer Database: GALNT1 |
* 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 | |
REACTOME_METABOLISM_OF_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GALNT1 |
MedGen: GALNT1 (Human Medical Genetics with Condition) | |
ClinVar: GALNT1 | |
Phenotype | MGI: GALNT1 (International Mouse Phenotyping Consortium) |
PhenomicDB: GALNT1 |
Mutations for GALNT1 |
* 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 |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
- 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 |
pancreas | GALNT1 | chr18 | 33252683 | 33252703 | chr18 | 34365505 | 34365525 | |
pancreas | GALNT1 | chr18 | 33262421 | 33262441 | TMPRSS15 | chr21 | 19652827 | 19652847 |
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 GALNT1 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 |
BG289433 | GALNT1 | 1 | 557 | 18 | 33263387 | 33271068 | NFX1 | 552 | 638 | 9 | 33348276 | 33348363 | |
W52720 | GALNT1 | 1 | 63 | 18 | 33289677 | 33289739 | GALNT1 | 61 | 249 | 18 | 33283545 | 33289714 | |
DA662182 | ZSCAN30 | 1 | 122 | 18 | 32870095 | 32870216 | GALNT1 | 121 | 555 | 18 | 33263353 | 33269190 | |
AI952718 | PCYT1B | 13 | 287 | X | 24668190 | 24676354 | GALNT1 | 281 | 404 | 18 | 33270975 | 33271098 | |
AI656193 | PCYT1B | 13 | 287 | X | 24668190 | 24676354 | GALNT1 | 281 | 404 | 18 | 33270975 | 33271098 |
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=41) | (# total SNVs=16) |
(# 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 |
chr18:33243615-33243615 | p.H55Y | 2 |
chr18:33272189-33272189 | p.L402V | 2 |
chr18:33271056-33271056 | p.T353T | 2 |
chr18:33271142-33271142 | p.Y382C | 2 |
chr18:33272292-33272293 | p.? | 2 |
chr18:33272171-33272171 | p.I396V | 2 |
chr18:33257555-33257555 | p.G105G | 2 |
chr18:33234733-33234733 | p.K38fs*11 | 2 |
chr18:33263508-33263508 | p.C212F | 2 |
chr18:33283583-33283583 | p.N503N | 2 |
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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 | 1 | 2 |   | 4 | 2 |   | 2 |   | 1 |   |   | 3 | 6 | 3 | 1 |   | 4 | 5 | 1 | 10 |
# mutation | 1 | 2 |   | 4 | 2 |   | 2 |   | 1 |   |   | 3 | 6 | 3 | 1 |   | 4 | 5 | 1 | 12 |
nonsynonymous SNV | 1 |   |   | 3 | 1 |   | 1 |   | 1 |   |   | 3 | 2 | 2 | 1 |   | 4 | 4 |   | 9 |
synonymous SNV |   | 2 |   | 1 | 1 |   | 1 |   |   |   |   |   | 4 | 1 |   |   |   | 1 | 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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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 |
chr18:33271056 | p.T353T | 2 |
chr18:33263508 | p.C212F | 2 |
chr18:33243677 | p.G45R | 1 |
chr18:33283564 | p.L295P | 1 |
chr18:33263543 | p.D444H | 1 |
chr18:33271100 | p.H55Y | 1 |
chr18:33243730 | p.M313I | 1 |
chr18:33283583 | p.T478A | 1 |
chr18:33267013 | p.M75I | 1 |
chr18:33234650 | p.N320S | 1 |
Other DBs for Point Mutations |
Copy Number for GALNT1 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 GALNT1 |
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 |
CHST2,FSCN1,GALNT18,IL32,IL34,LMNA,LTBR, MIIP,MMP7,NFKB2,NFKBIE,PRKCDBP,RASSF4,RELB, RHOG,RPS6KA4,SLC25A22,TIMM44,TMEM39B,TWF2,TYMP | ADRA2C,ARHGAP23,ADM5,ACKR1,TMEM255B,GALNT18,GGT5, HDAC7,HYAL2,ID3,IFITM3,LPCAT4,MEGF6,MFNG, NOS3,PPM1F,RASIP1,SEMA6B,SLCO4A1,SPNS2,TMEM173 |
ADCY1,CLEC2B,DENND5A,FADS1,FADS3,FAM124A,FJX1, GAL,GALNT18,GPR63,GSTT2,ITPRIPL1,LDLRAD3,LOXL3, MAP7D3,NCDN,PGBD1,SAAL1,TMEM132A,TRIM65,TTYH2 | AKT3,ARHGAP23,C20orf194,DENND5A,FAM65A,GALNT18,GLI3, LRIG1,NFATC4,NFIX,NPR2,PBX3,PHLDB2,RILPL1, RUSC2,SHISA4,TBKBP1,TIMP2,TMEM109,ZBTB47,ZFPM2 |
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 GALNT1 |
There's no related Drug. |
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Cross referenced IDs for GALNT1 |
* 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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