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 CSGALNACT2
Basic gene info.Gene symbolCSGALNACT2
Gene namechondroitin sulfate N-acetylgalactosaminyltransferase 2
SynonymsCHGN2|GALNACT-2|GALNACT2
CytomapUCSC genome browser: 10q11.21
Genomic locationchr10 :43633933-43680749
Type of geneprotein-coding
RefGenesNM_018590.4,
Ensembl idENSG00000169826
Descriptionbeta 4 GalNAcT-2chondroitin beta1,4 N-acetylgalactosaminyltransferase 2
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000169826
HPRD : 11348
Vega : OTTHUMG00000018023
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CSGALNACT2
BioGPS: 55454
Gene Expression Atlas: ENSG00000169826
The Human Protein Atlas: ENSG00000169826
PathwayNCI Pathway Interaction Database: CSGALNACT2
KEGG: CSGALNACT2
REACTOME: CSGALNACT2
ConsensusPathDB
Pathway Commons: CSGALNACT2
MetabolismMetaCyc: CSGALNACT2
HUMANCyc: CSGALNACT2
RegulationEnsembl's Regulation: ENSG00000169826
miRBase: chr10 :43,633,933-43,680,749
TargetScan: NM_018590
cisRED: ENSG00000169826
ContextiHOP: CSGALNACT2
cancer metabolism search in PubMed: CSGALNACT2
UCL Cancer Institute: CSGALNACT2
Assigned class in ccmGDBC

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Phenotypic Information for CSGALNACT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CSGALNACT2
Familial Cancer Database: CSGALNACT2
* 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_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CSGALNACT2
MedGen: CSGALNACT2 (Human Medical Genetics with Condition)
ClinVar: CSGALNACT2
PhenotypeMGI: CSGALNACT2 (International Mouse Phenotyping Consortium)
PhenomicDB: CSGALNACT2

Mutations for CSGALNACT2
* 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 CSGALNACT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA381927CSGALNACT21396104365106343654362ACKR33975522237478468237489138
CN418454CSGALNACT21143104363394943650420PDXDC1142599161522744315228118
BQ637932CSGALNACT21537104365060943651145CDR2534621162235767822357765

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        1        
GAIN (# sample)        1        
LOSS (# sample)                 
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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=65)
Stat. for Synonymous SNVs
(# total SNVs=17)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr10:43659419-43659419p.L362F8
chr10:43659338-43659338p.T335T4
chr10:43654172-43654172p.R224H3
chr10:43678796-43678796p.P479S3
chr10:43651251-43651251p.F218F3
chr10:43651086-43651086p.L163L2
chr10:43662538-43662538p.Q416K2
chr10:43650762-43650762p.E55D2
chr10:43659339-43659339p.L336V2
chr10:43678849-43678849p.P496P2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 8  4 32 1131  73312
# mutation22 9  4 32 1431  103314
nonsynonymous SNV12 8  3 31 1131  42110
synonymous SNV1  1  1  1 3    6124
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
chr10:43654172p.Q416K2
chr10:43654238p.L163L2
chr10:43662538p.R224L2
chr10:43651086p.R246T2
chr10:43678849p.P496P2
chr10:43678731p.E526K1
chr10:43651227p.V26V1
chr10:43654346p.G144V1
chr10:43650711p.I267I1
chr10:43662480p.Q416R1

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 CSGALNACT2 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 CSGALNACT2

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

BACH1,BICC1,CLIC4,CSGALNACT2,DDX21,DSE,FERMT2,
FUT11,ITGB1,KCTD20,LATS2,LIMS1,LOX,MAP3K2,
PLXNC1,QKI,RIF1,RRAGC,SEC23A,SGTB,ZNF699
ACAP2,ACTR2,ATP11C,BNIP2,CCDC88A,CDC27,CEP170,
CSGALNACT2,EEA1,EXOC5,GNA13,KIAA1033,BLOC1S6,RAB8B,
RBMS1,RECQL,SGMS1,SGTB,SOCS4,SYNJ1,TMX3

VSTM4,C1S,CSGALNACT2,DZIP1,ENTPD1,EVC,FSTL1,
GAS7,GNB4,GPC6,LUM,MAF,MCC,NR3C1,
PDGFRB,PKD2,QKI,SULF1,TCF4,ZEB2,ZNF521
CALU,CEP170,CHN1,CSGALNACT2,DENND5A,ELOVL5,FKBP14,
GPR155,HECTD2,KCNE4,SLC9B2,PITPNB,PRKD3,QKI,
RAB11FIP2,RBMS1,RHOQ,SLC39A6,TBCEL,TCEAL4,TCF4
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 CSGALNACT2


There's no related Drug.
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Cross referenced IDs for CSGALNACT2
* 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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