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 GALNT3
Basic gene info.Gene symbolGALNT3
Gene namepolypeptide N-acetylgalactosaminyltransferase 3
SynonymsGalNAc-T3|HFTC|HHS
CytomapUCSC genome browser: 2q24-q31
Genomic locationchr2 :166604312-166650803
Type of geneprotein-coding
RefGenesNM_004482.3,
Ensembl idENSG00000115339
DescriptionGalNAc transferase 3UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 3UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)polypeptide GalNAc transferase 3polypeptide GalNAc-transferase T3pp-GaNTase 3
Modification date20141219
dbXrefs MIM : 601756
HGNC : HGNC
Ensembl : ENSG00000115339
HPRD : 03453
Vega : OTTHUMG00000132157
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALNT3
BioGPS: 2591
Gene Expression Atlas: ENSG00000115339
The Human Protein Atlas: ENSG00000115339
PathwayNCI Pathway Interaction Database: GALNT3
KEGG: GALNT3
REACTOME: GALNT3
ConsensusPathDB
Pathway Commons: GALNT3
MetabolismMetaCyc: GALNT3
HUMANCyc: GALNT3
RegulationEnsembl's Regulation: ENSG00000115339
miRBase: chr2 :166,604,312-166,650,803
TargetScan: NM_004482
cisRED: ENSG00000115339
ContextiHOP: GALNT3
cancer metabolism search in PubMed: GALNT3
UCL Cancer Institute: GALNT3
Assigned class in ccmGDBC

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Phenotypic Information for GALNT3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALNT3
Familial Cancer Database: GALNT3
* 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: GALNT3
MedGen: GALNT3 (Human Medical Genetics with Condition)
ClinVar: GALNT3
PhenotypeMGI: GALNT3 (International Mouse Phenotyping Consortium)
PhenomicDB: GALNT3

Mutations for GALNT3
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryGALNT3chr2166629770166629790GALNT3chr2166604433166604453
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 GALNT3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF902896GALNT31542166611225166611481ABCA7522971910560821056413

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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=49)
Stat. for Synonymous SNVs
(# total SNVs=18)
Stat. for Deletions
(# total SNVs=2)
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
chr2:166621457-166621457p.L209F4
chr2:166618424-166618424p.D277H3
chr2:166621443-166621443p.P213P3
chr2:166627133-166627133p.V26V2
chr2:166621445-166621445p.P213S2
chr2:166621492-166621492p.A197V2
chr2:166621497-166621497p.N195N2
chr2:166613637-166613637p.R438C2
chr2:166626716-166626716p.G165G2
chr2:166615969-166615969p.N317S2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 152 4 2  821  65 8
# mutation 1 122 4 2  831  65 9
nonsynonymous SNV 1 9  3    831  32 8
synonymous SNV   32 1 2       33 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
chr2:166621443p.P213P3
chr2:166618451p.A268T2
chr2:166615969p.R553Q2
chr2:166606373p.E545K2
chr2:166606398p.G165G2
chr2:166626716p.N317S2
chr2:166611208p.D622H1
chr2:166626759p.H478Y1
chr2:166615260p.E271E1
chr2:166605329p.F29L1

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 GALNT3 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 GALNT3

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

ACTR3,AGFG1,CCNYL1,CMPK1,CREB3L2,FNDC3B,GALNT3,
GAN,GORASP2,IDH1,MFSD9,PEX13,PPP1CB,PPP2R3A,
PRKAA1,PSME4,RNF217,SLC31A1,SLC41A2,TES,TMEM123
ATP8B1,CDS1,ESRP1,ESRP2,GALNT3,GRAMD1C,GRHL2,
HOOK1,IRF6,KIAA0895,MAP7,MARVELD2,PLS1,RBM47,
SDR42E1,SHROOM3,TEX9,TFAP2A,TMEM30B,ZNF649,ZSWIM5

AGR2,ALDH1L1,ANG,BCAS1,C4orf19,SMIM14,CREB3L1,
FAM177B,GALNT12,GALNT3,GALNT7,GNE,FFAR4,KDELR3,
MRAP2,RNASE4,SLC35A1,SRD5A3,TC2N,TSPAN13,UAP1
ACBD3,ATP2C1,BRCC3,CMTM8,DENND2D,EDEM3,EHF,
ESRP1,FOXA3,GALNT3,ICA1,KDELR2,LXN,PAWR,
SLC10A7,SLC35A2,TM9SF2,TPD52,TSPAN13,TTC39A,ZDHHC13
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 GALNT3


There's no related Drug.
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Cross referenced IDs for GALNT3
* 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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