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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GALNT7 |
Basic gene info. | Gene symbol | GALNT7 |
Gene name | polypeptide N-acetylgalactosaminyltransferase 7 | |
Synonyms | GALNAC-T7|GalNAcT7 | |
Cytomap | UCSC genome browser: 4q31.1 | |
Genomic location | chr4 :174089903-174245118 | |
Type of gene | protein-coding | |
RefGenes | NM_017423.2, | |
Ensembl id | ENSG00000109586 | |
Description | N-acetylgalactosaminyltransferase 7UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 7UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)polypeptide GalNAc transferase 7pp-GaNTase 7protein-UDP acetylg | |
Modification date | 20141207 | |
dbXrefs | MIM : 605005 | |
HGNC : HGNC | ||
Ensembl : ENSG00000109586 | ||
HPRD : 10386 | ||
Vega : OTTHUMG00000160817 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GALNT7 | |
BioGPS: 51809 | ||
Gene Expression Atlas: ENSG00000109586 | ||
The Human Protein Atlas: ENSG00000109586 | ||
Pathway | NCI Pathway Interaction Database: GALNT7 | |
KEGG: GALNT7 | ||
REACTOME: GALNT7 | ||
ConsensusPathDB | ||
Pathway Commons: GALNT7 | ||
Metabolism | MetaCyc: GALNT7 | |
HUMANCyc: GALNT7 | ||
Regulation | Ensembl's Regulation: ENSG00000109586 | |
miRBase: chr4 :174,089,903-174,245,118 | ||
TargetScan: NM_017423 | ||
cisRED: ENSG00000109586 | ||
Context | iHOP: GALNT7 | |
cancer metabolism search in PubMed: GALNT7 | ||
UCL Cancer Institute: GALNT7 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for GALNT7(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GALNT7 |
Familial Cancer Database: GALNT7 |
* 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: GALNT7 |
MedGen: GALNT7 (Human Medical Genetics with Condition) | |
ClinVar: GALNT7 | |
Phenotype | MGI: GALNT7 (International Mouse Phenotyping Consortium) |
PhenomicDB: GALNT7 |
Mutations for GALNT7 |
* 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 | GALNT7 | chr4 | 174148953 | 174148973 | GALNT7 | chr4 | 174149168 | 174149188 |
pancreas | GALNT7 | chr4 | 174121120 | 174121140 | GALNT7 | chr4 | 174122694 | 174122714 |
pancreas | GALNT7 | chr4 | 174129045 | 174129065 | GALNT7 | chr4 | 174130717 | 174130737 |
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 GALNT7 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 |
BQ004985 | GALNT7 | 132 | 151 | 4 | 174137341 | 174137360 | COL1A2 | 143 | 552 | 7 | 94043007 | 94047144 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |
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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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=58) | (# total SNVs=14) |
(# total SNVs=0) | (# 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 |
chr4:174090004-174090004 | p.G6G | 4 |
chr4:174169388-174169388 | p.R128R | 3 |
chr4:174213410-174213410 | p.D247N | 3 |
chr4:174216610-174216610 | p.R273Q | 3 |
chr4:174216643-174216643 | p.R284Q | 2 |
chr4:174216978-174216978 | p.P317T | 2 |
chr4:174238797-174238797 | p.E541K | 2 |
chr4:174235124-174235124 | p.V469M | 2 |
chr4:174169569-174169569 | p.V189I | 2 |
chr4:174223217-174223217 | p.G390R | 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 | 3 |   | 8 | 1 |   |   |   | 5 |   | 1 | 6 | 1 |   |   |   | 5 | 2 | 2 | 9 |
# mutation | 1 | 3 |   | 8 | 1 |   |   |   | 5 |   | 1 | 7 | 1 |   |   |   | 6 | 2 | 2 | 8 |
nonsynonymous SNV | 1 | 2 |   | 6 |   |   |   |   | 5 |   |   | 5 |   |   |   |   | 5 |   | 1 | 8 |
synonymous SNV |   | 1 |   | 2 | 1 |   |   |   |   |   | 1 | 2 | 1 |   |   |   | 1 | 2 | 1 |   |
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 |
chr4:174213410 | p.D247N | 3 |
chr4:174216610 | p.R284Q | 2 |
chr4:174238797 | p.E541K | 2 |
chr4:174216643 | p.R273Q | 2 |
chr4:174219377 | p.G77G | 1 |
chr4:174169178 | p.R276G | 1 |
chr4:174223291 | p.E418Q | 1 |
chr4:174169582 | p.L82I | 1 |
chr4:174219381 | p.P434S | 1 |
chr4:174169235 | p.S84C | 1 |
Other DBs for Point Mutations |
Copy Number for GALNT7 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 GALNT7 |
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 |
ALDH6A1,ATP8B1,SMIM14,C9orf152,C9orf91,CCDC160,CD46, EDEM3,EIF2AK3,ENTPD3,FOXA1,GALNT7,KIAA1244,LRRC31, LRRFIP1,MIA3,SEC16A,SEC62,SETD7,SLC44A4,TMEM87B | ALCAM,ARSD,ATP8B1,CCDC160,CORO2A,EPT1,GALNT3, GALNT7,HOOK1,MAP7,MARVELD2,MYO5B,OCLN,PPM1H, RBM47,SHROOM3,SLC38A1,STRBP,TEX9,TMEM87B,TOM1L1 | ||||
AGR2,ANG,ATP2A3,ATP8B1,SMIM14,CAMK2D,CAPN9, CD55,CREB3L1,GALNT3,GALNT7,MLPH,MRAP2,REG4, RNASE4,SIDT1,SRD5A3,ST3GAL4,TC2N,UAP1,ZBTB7C | ACVR1B,ADAM10,AHCYL2,BCL2L11,CDH1,DSG2,EPB41L4B, GALNT12,GALNT7,LGR4,LIMA1,NCEH1,PIGG,PLD1, PPAPDC2,PPM1B,RAVER2,SH3BGRL2,SNX30,SYTL2,TMEM87B |
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 GALNT7 |
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 |
DB01033 | UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7) | approved | Mercaptopurine | ||
DB00563 | UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7) | approved | Methotrexate |
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Cross referenced IDs for GALNT7 |
* 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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