Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 GALNT13
Basic gene info.Gene symbolGALNT13
Gene namepolypeptide N-acetylgalactosaminyltransferase 13
SynonymsGalNAc-T13
CytomapUCSC genome browser: 2q24.1
Genomic locationchr2 :154728425-155310489
Type of geneprotein-coding
RefGenesNM_001301627.1,
NM_052917.3,
Ensembl idENSG00000144278
DescriptionGalNAc transferase 13UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 13UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)polypeptide GalNAc transferase 13pp-GaNTase 13protein-UDP acetylgalactosam
Modification date20141207
dbXrefs MIM : 608369
HGNC : HGNC
Ensembl : ENSG00000144278
HPRD : 16325
Vega : OTTHUMG00000131917
ProteinUniProt: Q8IUC8
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALNT13
BioGPS: 114805
Gene Expression Atlas: ENSG00000144278
The Human Protein Atlas: ENSG00000144278
PathwayNCI Pathway Interaction Database: GALNT13
KEGG: GALNT13
REACTOME: GALNT13
ConsensusPathDB
Pathway Commons: GALNT13
MetabolismMetaCyc: GALNT13
HUMANCyc: GALNT13
RegulationEnsembl's Regulation: ENSG00000144278
miRBase: chr2 :154,728,425-155,310,489
TargetScan: NM_001301627
cisRED: ENSG00000144278
ContextiHOP: GALNT13
cancer metabolism search in PubMed: GALNT13
UCL Cancer Institute: GALNT13
Assigned class in ccmGDBB - This gene belongs to cancer gene.

Top
Phenotypic Information for GALNT13(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALNT13
Familial Cancer Database: GALNT13
* 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 608369; gene.
Orphanet
DiseaseKEGG Disease: GALNT13
MedGen: GALNT13 (Human Medical Genetics with Condition)
ClinVar: GALNT13
PhenotypeMGI: GALNT13 (International Mouse Phenotyping Consortium)
PhenomicDB: GALNT13

Mutations for GALNT13
* 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
liverGALNT13chr2155281309155281309chr102923328329233283
ovaryGALNT13chr2154792030154792050GALNT13chr2154795397154795417
ovaryGALNT13chr2154897514154897534GALNT13chr2154929979154929999
ovaryGALNT13chr2154898956154898976GALNT13chr2154899103154899123
ovaryGALNT13chr2155060396155060416GALNT13chr2155225724155225744
ovaryGALNT13chr2155069331155069351GALNT13chr2155069561155069581
ovaryGALNT13chr2155154989155155189GALNT13chr2155155282155155482
ovaryGALNT13chr2155155018155155038GALNT13chr2155155421155155441
ovaryGALNT13chr2155199393155199413GALNT13chr2155201245155201265
ovaryGALNT13chr2155203494155203514GALNT13chr2155200879155200899
ovaryGALNT13chr2155280058155280078GALNT13chr2155282761155282781
pancreasGALNT13chr2155200929155200949GALNT13chr2155200866155200886
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 GALNT13 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM931973AKAP916033379172592991726102GALNT133193382155004397155004416
Z97017GALNT13115852155153258155154839USP341585174826147951661479679
DW462544GALNT13172192155100531155100733GALNT132183682155099822155099972
BF665493PRKCA1387176451141164511798GALNT133683942154989282154989308

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample12 23 5 4 1    11
GAIN (# sample)12 13   1 1    11
LOSS (# sample)   1  5 3        
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)

Top
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=4

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=147)
Stat. for Synonymous SNVs
(# total SNVs=29)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr2:155102455-155102455p.E273*4
chr2:155098678-155098678p.E149D4
chr2:155157982-155157982p.R346W4
chr2:155158006-155158006p.P354S3
chr2:155098590-155098590p.V120A3
chr2:155295140-155295140p.D478N3
chr2:155102432-155102432p.R265H3
chr2:155099233-155099233p.E167E2
chr2:155115621-155115621p.W315*2
chr2:154996876-154996876p.P57T2

Top
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
# sample12 173 5 5  19154 12810 12
# mutation12 193 6 5  26154 13210 15
nonsynonymous SNV12 142 5 3  24123  237 12
synonymous SNV   51 1 2  231 193 3
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])

Top
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
chr2:155158006p.P354S3
chr2:155295167p.G306E2
chr2:155115593p.R476Q2
chr2:155158018p.R265H2
chr2:155102432p.E167E2
chr2:155099233p.L487F2
chr2:155099239p.Y169Y2
chr2:154801126p.E39G2
chr2:155295135p.G358C2
chr2:155115588p.E304D2

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 GALNT13 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]

Top
Gene Expression for GALNT13

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

: Open all plots for all cancer types


Top
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

CHRM3,FLJ23867,FOXC1,FZD7,GALNT13,GLP1R,ITGA6,
KCNN4,KCNS1,LPO,MFI2,MIA,PDIA2,PRR4,
PTH2R,SMR3A,SMR3B,SOX10,SOX6,TMEM74,TMX4
AKAP12,CLMP,MTURN,DDHD2,DOCK11,EHBP1,EPB41L2,
FAM92A1,GALNT13,GCOM1,GLYAT,ITSN1,MARK1,NMT2,
PALM2-AKAP2,PALMD,PCDH9,PYGL,SAR1A,SEPT11,STX7

BEX1,C11orf16,LINC00523,CACNA1I,CD8B,CYMP,DKK4,
DPT,DSCR10,EPHA8,FER1L5,GALNT13,KRTAP19-8,LECT1,
MAGEB10,MAGEB2,MBD3L1,C7orf62,MOG,NELL1,RBP3
ANO3,ATCAY,ATP2B2,DIRAS2,ECM2,FGF14,FZD7,
GALNT13,GARNL3,GRIA2,HMP19,HS6ST3,NAPB,NDRG4,
PHOX2B,PPP2R2C,PRIMA1,SYT1,SYT5,SYT9,TPPP3
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for GALNT13


There's no related Drug.
Top
Cross referenced IDs for GALNT13
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas