Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for C1GALT1
Basic gene info.Gene symbolC1GALT1
Gene namecore 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1
SynonymsC1GALT|T-synthase
CytomapUCSC genome browser: 7p21.3
Genomic locationchr7 :7222245-7288251
Type of geneprotein-coding
RefGenesNM_020156.4,
Ensembl idENSG00000106392
DescriptionB3Gal-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 date20141207
dbXrefs MIM : 610555
HGNC : HGNC
Ensembl : ENSG00000106392
HPRD : 16631
Vega : OTTHUMG00000151912
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_C1GALT1
BioGPS: 56913
Gene Expression Atlas: ENSG00000106392
The Human Protein Atlas: ENSG00000106392
PathwayNCI Pathway Interaction Database: C1GALT1
KEGG: C1GALT1
REACTOME: C1GALT1
ConsensusPathDB
Pathway Commons: C1GALT1
MetabolismMetaCyc: C1GALT1
HUMANCyc: C1GALT1
RegulationEnsembl's Regulation: ENSG00000106392
miRBase: chr7 :7,222,245-7,288,251
TargetScan: NM_020156
cisRED: ENSG00000106392
ContextiHOP: C1GALT1
cancer metabolism search in PubMed: C1GALT1
UCL Cancer Institute: C1GALT1
Assigned class in ccmGDBC

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Phenotypic Information for C1GALT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: C1GALT1
Familial Cancer Database: C1GALT1
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: C1GALT1
MedGen: C1GALT1 (Human Medical Genetics with Condition)
ClinVar: C1GALT1
PhenotypeMGI: C1GALT1 (International Mouse Phenotyping Consortium)
PhenomicDB: C1GALT1

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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastC1GALT1chr772723507272350KIAA1598chr10118780671118780671
ovaryC1GALT1chr772245077224527C1GALT1chr772812557281275
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows C1GALT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AL134316C1GALT12075772872187287273C1GALT174386772872517287563

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample     11 3    11  
GAIN (# sample)     11 2    11  
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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=17)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr7:7278024-7278024p.F120C2
chr7:7283256-7283256p.G330G2
chr7:7278079-7278079p.E138E2
chr7:7283162-7283162p.G299V2
chr7:7278181-7278181p.T172T2
chr7:7278461-7278461p.F266I1
chr7:7283232-7283232p.L322L1
chr7:7278199-7278199p.N178K1
chr7:7278468-7278468p.P268H1
chr7:7283247-7283247p.R327R1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2114  2 1  2    5411
# mutation2114  2 1  2    6512
nonsynonymous SNV1111  2 1  2    4412
synonymous SNV1  3            21  
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr7:7283267p.S307F1
chr7:7278086p.D141Y1
chr7:7278375p.H309Y1
chr7:7283290p.D169Y1
chr7:7278170p.Y310C1
chr7:7278461p.D169E1
chr7:7283346p.L322L1
chr7:7278172p.T172T1
chr7:7278468p.R327R1
chr7:7278181p.D177H1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

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
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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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

: Open all cross reference information



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