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 GALNT9
Basic gene info.Gene symbolGALNT9
Gene namepolypeptide N-acetylgalactosaminyltransferase 9
SynonymsGALNAC-T9|GALNACT9
CytomapUCSC genome browser: 12q24.33
Genomic locationchr12 :132680916-132690573
Type of geneprotein-coding
RefGenesNM_001122636.1,
NM_021808.3,
Ensembl idENSG00000259919
DescriptionGalNAc transferase 9UDP-GalNAc: polypeptide N-acetylgalactosaminyltransferase 9UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 9UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)polypeptide GalNAc t
Modification date20141207
dbXrefs MIM : 606251
HGNC : HGNC
Ensembl : ENSG00000182870
Vega : OTTHUMG00000168256
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALNT9
BioGPS: 50614
Gene Expression Atlas: ENSG00000259919
The Human Protein Atlas: ENSG00000259919
PathwayNCI Pathway Interaction Database: GALNT9
KEGG: GALNT9
REACTOME: GALNT9
ConsensusPathDB
Pathway Commons: GALNT9
MetabolismMetaCyc: GALNT9
HUMANCyc: GALNT9
RegulationEnsembl's Regulation: ENSG00000259919
miRBase: chr12 :132,680,916-132,690,573
TargetScan: NM_001122636
cisRED: ENSG00000259919
ContextiHOP: GALNT9
cancer metabolism search in PubMed: GALNT9
UCL Cancer Institute: GALNT9
Assigned class in ccmGDBC

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Phenotypic Information for GALNT9(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALNT9
Familial Cancer Database: GALNT9
* 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: GALNT9
MedGen: GALNT9 (Human Medical Genetics with Condition)
ClinVar: GALNT9
PhenotypeMGI: GALNT9 (International Mouse Phenotyping Consortium)
PhenomicDB: GALNT9

Mutations for GALNT9
* 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 GALNT9 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=32)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr12:132683771-132683771p.A116G5
chr12:132682414-132682414p.G164S3
chr12:132688167-132688167p.R16R2
chr12:132688080-132688080p.H45H2
chr12:132685685-132685685p.T96S2
chr12:132683761-132683761p.G119G2
chr12:132688129-132688129p.R29H2
chr12:132685783-132685783p.D63D2
chr12:132681656-132681656p.H237P1
chr12:132688069-132688069p.A49V1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample14 82      42   64 6
# mutation14 82      42   64 9
nonsynonymous SNV13 82      11   54 8
synonymous SNV 1         31   1  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
chr12:132685783p.D63E,GALNT92
chr12:132681656p.A163V1
chr12:132688193p.A178V,GALNT91
chr12:132683752p.R77C,GALNT91
chr12:132681657p.A147T1
chr12:132824506p.R167C,GALNT91
chr12:132683763p.R71H,GALNT91
chr12:132688051p.D106E1
chr12:132681707p.G164S,GALNT91
chr12:132824533p.E61A1

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 GALNT9 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 GALNT9

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

ABCG4,ADAM11,ADCYAP1R1,BPIFB4,CACNA1G,EBF2,EPHA5,
FAM163A,GALNT9,IGF2-AS,INS-IGF2,ISLR2,ITM2A,KCNQ2,
KRT3,LPPR4,OR14C36,OR2T4,PCDHGA9,TRPC5,VAT1L
ASB6,SMG9,CCDC88B,CDK3,CHTF18,FAM53A,FUT6,
GALNT9,GTPBP3,KAT2A,KCNN4,KLHL17,LOC100129637,MYEOV,
NEIL1,NSUN5P1,RBM19,RECQL5,TRAF2,TRMT2A,ZNF133

ALPP,ALPPL2,CCDC63,CGB,CGB5,CST13P,FAM25A,
GALNT9,GAST,KCP,KLK7,KRT4,LOC100130238,LOC100131726,
LOC254312,LOC283404,LOC644172,MESP2,PADI1,SRL,TTBK1
ASIC1,ATP1A2,NPR3,CNTNAP5,DACT3,PIEZO2,GALNT9,
GJC2,GPR26,JMY,KY,LOC158696,NPTXR,NRXN2,
NTSR1,ODAM,OLFML2A,PEG10,PLCD4,PLCL1,PYGM
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 GALNT9


There's no related Drug.
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Cross referenced IDs for GALNT9
* 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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