Cancer Cell Metabolism Gene Database

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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 GALNT5
Basic gene info.Gene symbolGALNT5
Gene namepolypeptide N-acetylgalactosaminyltransferase 5
SynonymsGALNAC-T5|GALNACT5
CytomapUCSC genome browser: 2q24.1
Genomic locationchr2 :158114339-158167913
Type of geneprotein-coding
RefGenesNM_014568.1,
Ensembl idENSG00000136542
DescriptionUDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 5UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)polypeptide GalNAc transferase 5pp-GaNTase 5protein-UDP acetylgalactosaminyltransferase 5
Modification date20141207
dbXrefs MIM : 615129
HGNC : HGNC
HPRD : 09970
ProteinUniProt: Q7Z7M9
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALNT5
BioGPS: 11227
Gene Expression Atlas: ENSG00000136542
The Human Protein Atlas: ENSG00000136542
PathwayNCI Pathway Interaction Database: GALNT5
KEGG: GALNT5
REACTOME: GALNT5
ConsensusPathDB
Pathway Commons: GALNT5
MetabolismMetaCyc: GALNT5
HUMANCyc: GALNT5
RegulationEnsembl's Regulation: ENSG00000136542
miRBase: chr2 :158,114,339-158,167,913
TargetScan: NM_014568
cisRED: ENSG00000136542
ContextiHOP: GALNT5
cancer metabolism search in PubMed: GALNT5
UCL Cancer Institute: GALNT5
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GALNT5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALNT5
Familial Cancer Database: GALNT5
* 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: GALNT5
MedGen: GALNT5 (Human Medical Genetics with Condition)
ClinVar: GALNT5
PhenotypeMGI: GALNT5 (International Mouse Phenotyping Consortium)
PhenomicDB: GALNT5

Mutations for GALNT5
* 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
ovaryGALNT5chr2158114577158114597chr2157076182157076202
pancreasGALNT5chr2158147128158147148GALNT5chr2158147798158147818
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 GALNT5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF109407PABPC46919114003347140034548GALNT51783512158115681158115854

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 # sample11               
GAIN (# sample) 1               
LOSS (# sample)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=10

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=90)
Stat. for Synonymous SNVs
(# total SNVs=24)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr2:158142577-158142577p.R558W5
chr2:158156137-158156137p.L692P4
chr2:158156138-158156138p.L692L4
chr2:158115271-158115271p.R226K3
chr2:158157422-158157422p.R784*3
chr2:158115636-158115636p.P348S2
chr2:158115906-158115906p.P438S2
chr2:158157217-158157217p.I715I2
chr2:158115364-158115364p.K257T2
chr2:158140860-158140860p.E507D2

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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=8

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample353222 5 4  117 1 119 12
# mutation353202 5 4  117 1 1211 12
nonsynonymous SNV332161 3 4  86   88 6
synonymous SNV 2141 2    31 1 43 6
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
chr2:158156137p.L692P4
chr2:158156138p.L692L4
chr2:158142577p.R558W3
chr2:158157217p.T420T2
chr2:158115854p.R226K2
chr2:158115271p.K257T2
chr2:158115364p.I715I2
chr2:158115519p.G309R2
chr2:158115201p.H128L1
chr2:158142597p.K349K1

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 GALNT5 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 GALNT5

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

ENPP5,ENTPD3,FUCA1,GALNT5,GALNT7,GDF9,GPD2,
IQGAP2,KAL1,LOC494141,LOC728606,LRRC31,MRGPRX4,MYO3B,
MYOD1,NEK10,P2RY4,PTPLAD2,SCUBE2,SPATA6,VWA2
BRIP1,CEACAM1,COL27A1,CSRNP3,EHF,ERN1,FAM196B,
FAM83B,GALNT5,KIF24,LY75,RCAN3,RFWD3,RPGRIP1L,
SHANK2,SLC9A7,SMARCC1,SYNJ2,TCF20,TEX9,TRPS1

ADAM9,ARFGAP3,ASAP2,CD55,CREB3L1,DOCK5,FAM114A1,
GAREM,GALNT5,GPD2,FFAR4,KDELR3,LIPH,LRP10,
MAP3K6,MLPH,PLXNB2,RAB27B,SEC24D,SGMS2,SHROOM3
CKAP4,CREB3L1,FAM177B,FOXA2,GALNT5,FFAR4,JPH1,
MAP3K5,MCF2L,MLPH,MUC12,QSOX1,SCEL,SIDT1,
SLC12A8,SLC17A9,SLC39A7,SLC45A3,SPON1,ST3GAL4,TTC39A
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 GALNT5


There's no related Drug.
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Cross referenced IDs for GALNT5
* 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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