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 GALNT10
Basic gene info.Gene symbolGALNT10
Gene namepolypeptide N-acetylgalactosaminyltransferase 10
SynonymsGALNACT10|PPGALNACT10|PPGANTASE10
CytomapUCSC genome browser: 5q33.2
Genomic locationchr5 :153570294-153800543
Type of geneprotein-coding
RefGenesNM_198321.3,
NM_017540.3,NM_024564.1,
Ensembl idENSG00000164574
DescriptionGalNAc transferase 10UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 10UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)
Modification date20141207
dbXrefs MIM : 608043
HGNC : HGNC
Ensembl : ENSG00000164574
HPRD : 12157
Vega : OTTHUMG00000130145
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALNT10
BioGPS: 55568
Gene Expression Atlas: ENSG00000164574
The Human Protein Atlas: ENSG00000164574
PathwayNCI Pathway Interaction Database: GALNT10
KEGG: GALNT10
REACTOME: GALNT10
ConsensusPathDB
Pathway Commons: GALNT10
MetabolismMetaCyc: GALNT10
HUMANCyc: GALNT10
RegulationEnsembl's Regulation: ENSG00000164574
miRBase: chr5 :153,570,294-153,800,543
TargetScan: NM_198321
cisRED: ENSG00000164574
ContextiHOP: GALNT10
cancer metabolism search in PubMed: GALNT10
UCL Cancer Institute: GALNT10
Assigned class in ccmGDBC

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Phenotypic Information for GALNT10(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALNT10
Familial Cancer Database: GALNT10
* 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: GALNT10
MedGen: GALNT10 (Human Medical Genetics with Condition)
ClinVar: GALNT10
PhenotypeMGI: GALNT10 (International Mouse Phenotyping Consortium)
PhenomicDB: GALNT10

Mutations for GALNT10
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastGALNT10chr5153763540153763540chr127146229471462294
ovaryGALNT10chr5153766697153766717chr191149883511498855
ovaryGALNT10chr5153766815153766835chr5154696202154696222
pancreasGALNT10chr5153658912153659112CBLchr11119124194119124394
pancreasGALNT10chr5153666875153666895chr5159343243159343263
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 GALNT10 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF155072GALNT1011165153800378153800494GALNT101174725153799900153800255
DA949043GALNT1013055153778005153778307MYH9302557223670759936707854

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 # sample13    9 4 1 1 11 
GAIN (# sample) 1    1 3   1 1  
LOSS (# sample)12    8 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=4

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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=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
chr5:153755896-153755896p.R210*3
chr5:153709146-153709146p.R139H3
chr5:153765888-153765888p.A318A2
chr5:153765900-153765900p.F322F2
chr5:153755919-153755919p.L217L2
chr5:153760081-153760081p.Y276Y2
chr5:153792479-153792479p.D473H2
chr5:153677535-153677535p.T99T2
chr5:153789197-153789197p.A421T2
chr5:153789216-153789216p.R427H2

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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
# sample 21101 2 31 73  378110
# mutation 2191 2 31 73  378110
nonsynonymous SNV 2 61 1 11 43  24417
synonymous SNV  13  1 2  3   134 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])

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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
chr5:153765879p.D273N2
chr5:153765888p.P315P2
chr5:153755919p.A318A2
chr5:153765900p.F322F2
chr5:153760070p.I349I2
chr5:153765981p.D76N2
chr5:153674442p.L217L2
chr5:153760181p.P264R1
chr5:153783767p.A387G1
chr5:153674472p.Q586Q1

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 GALNT10 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 GALNT10

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

ARHGEF38,ATXN1,BNC2,KIAA0825,CTNNA1,EVC,FAM114A2,
FBN1,FYCO1,GALNT10,ARHGAP35,GXYLT2,KIAA0247,LIMA1,
LOC100129034,MFAP3,PRICKLE2,RAB27B,SH3D19,SLC24A2,YIPF5
ADAM10,ATRN,C12orf49,CACNA1D,CHST15,EDARADD,GALNT10,
LTBP2,MAGI3,MICALCL,MYOF,PTPRJ,RAB27B,RASEF,
SEPT8,SFMBT2,SIPA1L1,SLC2A10,TTC26,TXLNA,WWC3

ACVR1,AFF4,ARHGAP26,CTNNA1,ECM1,EPAS1,GALNT10,
GALNT2,CEMIP,KIF26B,LAMB1,LAMC1,MAP4,MAST4,
MEGF8,NDST1,SDC3,SH3PXD2A,SH3PXD2B,TGFBI,TNKS1BP1
ABHD2,ACLY,ASCC3,EIF4G1,EPRS,GALNT10,GANAB,
MKI67,PDE11A,PRKDC,SBNO1,SEC16A,SEC24C,SEC61A1,
SMC1A,STT3A,TAF15,TMEM214,TRIP11,UGGT1,VPS53
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 GALNT10


There's no related Drug.
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Cross referenced IDs for GALNT10
* 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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