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 GALNT6
Basic gene info.Gene symbolGALNT6
Gene namepolypeptide N-acetylgalactosaminyltransferase 6
SynonymsGALNAC-T6|GalNAcT6
CytomapUCSC genome browser: 12q13
Genomic locationchr12 :51745832-51785200
Type of geneprotein-coding
RefGenesNM_007210.3,
Ensembl idENSG00000139629
DescriptionGalNAc transferase 6UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 6UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 6UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-
Modification date20141207
dbXrefs MIM : 605148
HGNC : HGNC
Ensembl : ENSG00000139629
HPRD : 05512
Vega : OTTHUMG00000185181
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALNT6
BioGPS: 11226
Gene Expression Atlas: ENSG00000139629
The Human Protein Atlas: ENSG00000139629
PathwayNCI Pathway Interaction Database: GALNT6
KEGG: GALNT6
REACTOME: GALNT6
ConsensusPathDB
Pathway Commons: GALNT6
MetabolismMetaCyc: GALNT6
HUMANCyc: GALNT6
RegulationEnsembl's Regulation: ENSG00000139629
miRBase: chr12 :51,745,832-51,785,200
TargetScan: NM_007210
cisRED: ENSG00000139629
ContextiHOP: GALNT6
cancer metabolism search in PubMed: GALNT6
UCL Cancer Institute: GALNT6
Assigned class in ccmGDBC

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Phenotypic Information for GALNT6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALNT6
Familial Cancer Database: GALNT6
* 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: GALNT6
MedGen: GALNT6 (Human Medical Genetics with Condition)
ClinVar: GALNT6
PhenotypeMGI: GALNT6 (International Mouse Phenotyping Consortium)
PhenomicDB: GALNT6

Mutations for GALNT6
* 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 GALNT6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK225124C316141967143646720616GALNT66092599125174714951758061
AI909009GALNT615325125174825251751944GALNT6321451125174790251748032

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 # sample   1            1
GAIN (# sample)   1            1
LOSS (# sample)                 
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=37)
Stat. for Synonymous SNVs
(# total SNVs=25)
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
chr12:51773357-51773357p.K70R3
chr12:51758021-51758021p.P311P3
chr12:51758030-51758030p.F308F3
chr12:51749712-51749712p.R545C3
chr12:51753078-51753078p.C402C2
chr12:51752037-51752037p.F459F2
chr12:51759245-51759245p.Q261Q2
chr12:51751178-51751178p.K520fs*792
chr12:51773084-51773084p.R161L2
chr12:51749711-51749711p.R545H2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample43 141 4 1  923 1202 4
# mutation43 121 4 1  1023 1272 5
nonsynonymous SNV1  71 3    622 1172 2
synonymous SNV33 5  1 1  4 1  10  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
chr12:51773357p.K70R3
chr12:51758021p.R161L2
chr12:51758030p.P311P2
chr12:51754561p.F308F2
chr12:51773084p.F459F2
chr12:51752037p.T371A2
chr12:51753107p.V405L1
chr12:51773181p.E338E1
chr12:51757921p.S199R1
chr12:51773463p.C527C1

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 GALNT6 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 GALNT6

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

C1orf64,CCDC125,CREB3L4,FBP1,FOXA1,GALNT6,GPR160,
INPP5J,LIMA1,PHOSPHO2,PRR15,SLC2A10,SLC44A4,SLC4A8,
SPDEF,TCEAL1,TCEAL3,TCEAL6,TRERF1,TRIM3,XBP1
AAGAB,ARSD,ARSG,DLG3,DNAJC12,ERBB3,FOXA1,
GALNT6,GOLM1,HHAT,KIAA0319L,LEO1,PRLR,PROM2,
RAB11FIP4,SEZ6L2,SLC4A8,SYTL2,VAV3,WNK4,ZYG11A

ACVR1B,APCDD1,AXIN2,CEACAM6,GALNT6,GUCY2C,ILDR1,
KRT23,MANSC1,MUC20,MYO1D,PRR15,REPS2,SAMD12,
SCARB1,SEMA5A,SLC4A8,SORL1,VWA2,WWP1,ZNF704
AQP3,CCDC108,CD82,CYP2J2,DAK,DNASE1,EMB,
GALNT6,KCNH6,LOC647121,MGAT3,MLXIPL,MST1,PFKFB4,
PLB1,RBP3,SERPINA1,SI,SLC28A2,TMEM92,ZNF488
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 GALNT6


There's no related Drug.
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Cross referenced IDs for GALNT6
* 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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