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 C1GALT1C1
Basic gene info.Gene symbolC1GALT1C1
Gene nameC1GALT1-specific chaperone 1
SynonymsC1GALT2|C38H2-L1|COSMC|MST143|TNPS
CytomapUCSC genome browser: Xq24
Genomic locationchrX :119759528-119764005
Type of geneprotein-coding
RefGenesNM_001011551.2,
NM_152692.4,
Ensembl idENSG00000171155
DescriptionC1Gal-T2C38H2-like protein 1beta 1,3-galactosyltransferase 2core 1 beta1,3-galactosyltransferase 2core 1 beta3-Gal-T2core 1 beta3-galactosyltransferase-specific molecular chaperone
Modification date20141207
dbXrefs MIM : 300611
HGNC : HGNC
Ensembl : ENSG00000171155
HPRD : 06462
Vega : OTTHUMG00000022305
ProteinUniProt: Q96EU7
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_C1GALT1C1
BioGPS: 29071
Gene Expression Atlas: ENSG00000171155
The Human Protein Atlas: ENSG00000171155
PathwayNCI Pathway Interaction Database: C1GALT1C1
KEGG: C1GALT1C1
REACTOME: C1GALT1C1
ConsensusPathDB
Pathway Commons: C1GALT1C1
MetabolismMetaCyc: C1GALT1C1
HUMANCyc: C1GALT1C1
RegulationEnsembl's Regulation: ENSG00000171155
miRBase: chrX :119,759,528-119,764,005
TargetScan: NM_001011551
cisRED: ENSG00000171155
ContextiHOP: C1GALT1C1
cancer metabolism search in PubMed: C1GALT1C1
UCL Cancer Institute: C1GALT1C1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for C1GALT1C1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: C1GALT1C1
Familial Cancer Database: C1GALT1C1
* 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 300611; gene.
300622; phenotype.
Orphanet
DiseaseKEGG Disease: C1GALT1C1
MedGen: C1GALT1C1 (Human Medical Genetics with Condition)
ClinVar: C1GALT1C1
PhenotypeMGI: C1GALT1C1 (International Mouse Phenotyping Consortium)
PhenomicDB: C1GALT1C1

Mutations for C1GALT1C1
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows C1GALT1C1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
T10800C1GALT1C1156X119760593119760648C1GALT1C149177X119760501119760634

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
There's no copy number variation information in COSMIC data for this gene.

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=21)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr23:119760629-119760629p.D131E3
chr23:119760717-119760717p.S102F2
chr23:119760722-119760722p.F100F1
chr23:119760270-119760270p.V251A1
chr23:119760538-119760538p.D162N1
chr23:119760807-119760807p.I72T1
chr23:119760273-119760273p.S250Y1
chr23:119760539-119760539p.K161N1
chr23:119760819-119760819p.R68Q1
chr23:119760290-119760290p.D244D1

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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
# sample11 3  1 1  12   36 5
# mutation11 3  1 1  12   36 5
nonsynonymous SNV11 3  1 1  11   24 4
synonymous SNV            1   12 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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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
chrX:119760717p.S102F,C1GALT1C12
chrX:119760273p.A143A,C1GALT1C11
chrX:119760819p.W139G,C1GALT1C11
chrX:119760290p.A129T,C1GALT1C11
chrX:119760844p.Y128Y,C1GALT1C11
chrX:119760440p.P312T,C1GALT1C11
chrX:119760846p.P311L,C1GALT1C11
chrX:119760538p.F100F,C1GALT1C11
chrX:119760874p.A298V,C1GALT1C11
chrX:119760088p.R68Q,C1GALT1C11

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 C1GALT1C1 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 C1GALT1C1

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 C1GALT1C1


There's no related Drug.
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Cross referenced IDs for C1GALT1C1
* 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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