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 GALNT2
Basic gene info.Gene symbolGALNT2
Gene namepolypeptide N-acetylgalactosaminyltransferase 2
SynonymsGalNAc-T2
CytomapUCSC genome browser: 1q41-q42
Genomic locationchr1 :230202955-230417875
Type of geneprotein-coding
RefGenesNM_001291866.1,
NM_004481.4,NR_120373.1,
Ensembl idENSG00000143641
DescriptionUDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 2UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)polypeptide GalNAc transferase 2pp-GaNTase 2
Modification date20141222
dbXrefs MIM : 602274
HGNC : HGNC
Ensembl : ENSG00000143641
HPRD : 03782
Vega : OTTHUMG00000037771
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALNT2
BioGPS: 2590
Gene Expression Atlas: ENSG00000143641
The Human Protein Atlas: ENSG00000143641
PathwayNCI Pathway Interaction Database: GALNT2
KEGG: GALNT2
REACTOME: GALNT2
ConsensusPathDB
Pathway Commons: GALNT2
MetabolismMetaCyc: GALNT2
HUMANCyc: GALNT2
RegulationEnsembl's Regulation: ENSG00000143641
miRBase: chr1 :230,202,955-230,417,875
TargetScan: NM_001291866
cisRED: ENSG00000143641
ContextiHOP: GALNT2
cancer metabolism search in PubMed: GALNT2
UCL Cancer Institute: GALNT2
Assigned class in ccmGDBC

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Phenotypic Information for GALNT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALNT2
Familial Cancer Database: GALNT2
* 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: GALNT2
MedGen: GALNT2 (Human Medical Genetics with Condition)
ClinVar: GALNT2
PhenotypeMGI: GALNT2 (International Mouse Phenotyping Consortium)
PhenomicDB: GALNT2

Mutations for GALNT2
* 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 GALNT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BJ995070ZNF66419812124457788124458467GALNT2926001230416045230416553
AW015340GALNT2112521230301660230301899AUTS224333176972294269723030
AW992137GALNT21771230272431230272507GALNT2763281230305798230306050
AF130059SMOC115330147035198470352299GALNT23226911230415455230415823
BG985354GALNT2273001230258147230258423BRD92935075882190882404
BQ335474GALNT2102801230398716230410299MEMO127433023221748132217537

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 # sample3  11 2 1   122 3
GAIN (# sample)2  11 1 1    21 3
LOSS (# sample)1     1     1 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=58)
Stat. for Synonymous SNVs
(# total SNVs=30)
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
chr1:230372444-230372444p.R194*3
chr1:230398367-230398367p.F395L3
chr1:230401027-230401027p.Q452*2
chr1:230372463-230372463p.R200Q2
chr1:230386265-230386265p.K323R2
chr1:230314000-230314000p.D55H2
chr1:230415081-230415081p.L531L2
chr1:230398658-230398658p.?2
chr1:230398700-230398700p.L421P2
chr1:230338999-230338999p.R113*2

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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
# sample341121 4 2211312 153 10
# mutation341131 4 2211312 153 13
nonsynonymous SNV21 101 3  11611  33 8
synonymous SNV1313  1 21 7 1 12  5
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
chr1:230381875p.L493L,GALNT22
chr1:230339028p.A228T,GALNT22
chr1:230398367p.F357L,GALNT22
chr1:230386265p.K285R,GALNT22
chr1:230415081p.R84R,GALNT22
chr1:230398728p.R341R,GALNT21
chr1:230372467p.I487I,GALNT21
chr1:230415090p.S120S,GALNT21
chr1:230338990p.N222T,GALNT21
chr1:230390970p.G227E,GALNT21

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 GALNT2 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 GALNT2

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

ADAM23,AVPI1,C1R,LINC00473,CAPN2,ECEL1,EXTL3,
FNDC3B,FNDC4,GALNT2,COLGALT1,GRAMD1B,H6PD,MCTP2,
PLOD3,PLXNA1,RAB4A,SNAP47,SYDE1,TAF5L,TNFRSF1A
AARS,AP2A1,B4GALT2,C1orf216,DCTN1,EHD1,GALNT2,
ITFG3,LAMB2,LRP3,MXD4,NUCB1,PKN1,PLXND1,
POR,RNPEPL1,RPS6KA4,ST3GAL2,TMEM104,USF2,ZBED1

ARAP3,ARHGEF11,ATF6,BCL9,CGNL1,GALNT2,GLUL,
GYLTL1B,IGF2,LAMA5,LRP1,MYO10,NCSTN,PI4KB,
PIK3C2B,SETDB1,SHC1,STRA6,STX6,TAF5L,ZNF687
AARS,ABCC1,LINC00346,CBX2,CLSTN3,DOC2B,ENG,
GALNT2,HK1,LRRC37A3,MAP3K6,MAPK11,MMRN2,PLXND1,
SELP,SLC43A3,SRP68,STAT5A,TNFRSF8,TXLNA,VCP
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 GALNT2


There's no related Drug.
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Cross referenced IDs for GALNT2
* 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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