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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for C1GALT1 |
Basic gene info. | Gene symbol | C1GALT1 |
Gene name | core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 | |
Synonyms | C1GALT|T-synthase | |
Cytomap | UCSC genome browser: 7p21.3 | |
Genomic location | chr7 :7222245-7288251 | |
Type of gene | protein-coding | |
RefGenes | NM_020156.4, | |
Ensembl id | ENSG00000106392 | |
Description | B3Gal-T8core 1 O-glycan T-synthasecore 1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase 1core 1 beta3-Gal-T1core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1glycoprotein-N-acetylgalactosam | |
Modification date | 20141207 | |
dbXrefs | MIM : 610555 | |
HGNC : HGNC | ||
Ensembl : ENSG00000106392 | ||
HPRD : 16631 | ||
Vega : OTTHUMG00000151912 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_C1GALT1 | |
BioGPS: 56913 | ||
Gene Expression Atlas: ENSG00000106392 | ||
The Human Protein Atlas: ENSG00000106392 | ||
Pathway | NCI Pathway Interaction Database: C1GALT1 | |
KEGG: C1GALT1 | ||
REACTOME: C1GALT1 | ||
ConsensusPathDB | ||
Pathway Commons: C1GALT1 | ||
Metabolism | MetaCyc: C1GALT1 | |
HUMANCyc: C1GALT1 | ||
Regulation | Ensembl's Regulation: ENSG00000106392 | |
miRBase: chr7 :7,222,245-7,288,251 | ||
TargetScan: NM_020156 | ||
cisRED: ENSG00000106392 | ||
Context | iHOP: C1GALT1 | |
cancer metabolism search in PubMed: C1GALT1 | ||
UCL Cancer Institute: C1GALT1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for C1GALT1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: C1GALT1 |
Familial Cancer Database: C1GALT1 |
* 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 |
Mutations for C1GALT1 |
* 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 |
breast | C1GALT1 | chr7 | 7272350 | 7272350 | KIAA1598 | chr10 | 118780671 | 118780671 |
ovary | C1GALT1 | chr7 | 7224507 | 7224527 | C1GALT1 | chr7 | 7281255 | 7281275 |
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 C1GALT1 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 |
AL134316 | C1GALT1 | 20 | 75 | 7 | 7287218 | 7287273 | C1GALT1 | 74 | 386 | 7 | 7287251 | 7287563 |
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 | 1 |   | 3 |   |   |   |   | 1 | 1 |   |   | |||
GAIN (# sample) |   |   |   |   |   | 1 | 1 |   | 2 |   |   |   |   | 1 | 1 |   |   | |||
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=17) | (# total SNVs=10) |
(# total SNVs=0) | (# 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 |
chr7:7278079-7278079 | p.E138E | 2 |
chr7:7283162-7283162 | p.G299V | 2 |
chr7:7278181-7278181 | p.T172T | 2 |
chr7:7278024-7278024 | p.F120C | 2 |
chr7:7283256-7283256 | p.G330G | 2 |
chr7:7278211-7278211 | p.L182L | 1 |
chr7:7278542-7278542 | p.P293S | 1 |
chr7:7283267-7283267 | p.R334I | 1 |
chr7:7278212-7278212 | p.L183I | 1 |
chr7:7278546-7278546 | p.P294H | 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 | 1 | 1 | 4 |   |   | 2 |   | 1 |   |   | 2 |   |   |   |   | 5 | 4 | 1 | 1 |
# mutation | 2 | 1 | 1 | 4 |   |   | 2 |   | 1 |   |   | 2 |   |   |   |   | 6 | 5 | 1 | 2 |
nonsynonymous SNV | 1 | 1 | 1 | 1 |   |   | 2 |   | 1 |   |   | 2 |   |   |   |   | 4 | 4 | 1 | 2 |
synonymous SNV | 1 |   |   | 3 |   |   |   |   |   |   |   |   |   |   |   |   | 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 |
chr7:7278468 | p.N178K | 1 |
chr7:7278181 | p.R334I | 1 |
chr7:7278537 | p.R180R | 1 |
chr7:7278194 | p.R342S | 1 |
chr7:7283162 | p.L182L | 1 |
chr7:7278199 | p.L360F | 1 |
chr7:7283186 | p.R196K | 1 |
chr7:7278205 | p.K217K | 1 |
chr7:7283191 | p.V224V | 1 |
chr7:7278211 | p.S237F | 1 |
Other DBs for Point Mutations |
Copy Number for C1GALT1 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 C1GALT1 |
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 |
AIFM1,ATG4A,ATP6AP2,C1GALT1C1,CETN2,CUL4B,CXorf56, LAMP2,LOC100303728,MCTS1,MOSPD1,MTM1,NKAP,OCRL, PSMD10,SLC25A5,TRMT2B,UBE2A,VMA21,ZBTB33,ZDHHC9 | ALG5,ARF4,ATP6AP2,C1GALT1C1,CALM2,CAPZA1,CDC42, ERLEC1,ERP44,KDELR2,LAPTM4A,MAPRE1,PPCS,PSMD10, RAB1A,RAC1,SLC35B3,TFG,TM2D2,XRCC4,YWHAB |
ARMCX5,ATP6AP2,BRCC3,C1GALT1C1,CUL4B,FAM104B,FUNDC2, HNRNPH2,LAMP2,MAGT1,MCTS1,MORF4L2,NKAP,NXT2, PGRMC1,PSMD10,RBMX2,SLC25A14,TSPAN6,UBE2A,VBP1 | ANXA7,ARPC3,ATG3,EMC7,C1GALT1C1,CISD2,GOLT1B, LOC653566,LSM6,MAGT1,MCTS1,POMP,PPA1,PSMA1, PSMA2,PSMA4,PSMA5,SCFD1,SSR3,TMED2,TMEM165 |
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 C1GALT1 |
There's no related Drug. |
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Cross referenced IDs for C1GALT1 |
* 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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