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 GALNTL6
Basic gene info.Gene symbolGALNTL6
Gene namepolypeptide N-acetylgalactosaminyltransferase-like 6
SynonymsGALNACT20|GALNT17|GalNAc-T6L
CytomapUCSC genome browser: 4q34.1
Genomic locationchr4 :172734574-173961558
Type of geneprotein-coding
RefGenesNM_001034845.2,
Ensembl idENSG00000174473
DescriptionGaNTase 17GalNAc transferase 17UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 17UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 20UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransfera
Modification date20141207
dbXrefs MIM : 615138
HGNC : HGNC
ProteinUniProt: Q49A17
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALNTL6
BioGPS: 442117
Gene Expression Atlas: ENSG00000174473
The Human Protein Atlas: ENSG00000174473
PathwayNCI Pathway Interaction Database: GALNTL6
KEGG: GALNTL6
REACTOME: GALNTL6
ConsensusPathDB
Pathway Commons: GALNTL6
MetabolismMetaCyc: GALNTL6
HUMANCyc: GALNTL6
RegulationEnsembl's Regulation: ENSG00000174473
miRBase: chr4 :172,734,574-173,961,558
TargetScan: NM_001034845
cisRED: ENSG00000174473
ContextiHOP: GALNTL6
cancer metabolism search in PubMed: GALNTL6
UCL Cancer Institute: GALNTL6
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GALNTL6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALNTL6
Familial Cancer Database: GALNTL6
* 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: GALNTL6
MedGen: GALNTL6 (Human Medical Genetics with Condition)
ClinVar: GALNTL6
PhenotypeMGI: GALNTL6 (International Mouse Phenotyping Consortium)
PhenomicDB: GALNTL6

Mutations for GALNTL6
* 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
ovaryGALNTL6chr4173360321173360341ODZ3chr4183552344183552364
pancreasGALNTL6chr4172826170172826370TMEM117chr124430212244302322
pancreasGALNTL6chr4173159682173159702RWDD4chr4184577119184577139
pancreasGALNTL6chr4173332792173332812GALNTL6chr4173332843173332863
pancreasGALNTL6chr4173476128173476148GALNTL6chr4173446207173446227
pancreasGALNTL6chr4173515480173515500chr11127818586127818606
pancreasGALNTL6chr4173723968173723988GALNTL6chr4173833423173833443
prostateGALNTL6chr4173233547173233547GALNTL6chr4173539655173539655
skinGALNTL6chr4173631903173631903GALNTL6chr4173632747173632747
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 GALNTL6 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample4211  1 3 1  14  
GAIN (# sample)211   1 1     1  
LOSS (# sample)21 1    2 1  13  
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=79)
Stat. for Synonymous SNVs
(# total SNVs=22)
Stat. for Deletions
(# total SNVs=4)
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
chr4:173961139-173961141p.K567delK3
chr4:173232893-173232893p.R126C3
chr4:173930333-173930333p.R459Q3
chr4:173873245-173873245p.R403W2
chr4:173150860-173150860p.L64L2
chr4:173803975-173803975p.D320Y2
chr4:173730599-173730599p.R214P2
chr4:173961153-173961153p.M570L2
chr4:173734719-173734719p.I256I2
chr4:173852374-173852374p.R368R2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample42213  5 1111751  1712 11
# mutation42213  5 1111851  1614 13
nonsynonymous SNV3 112  5 111124   1212 11
synonymous SNV1211       611  42 2
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
chr4:173930333p.R459Q3
chr4:173150860p.P446L2
chr4:173852374p.Q45E2
chr4:173734859p.R368R2
chr4:172735732p.R403W2
chr4:173873245p.M1V2
chr4:173873375p.L64F2
chr4:173232893p.M11I2
chr4:172735864p.L177I2
chr4:172735764p.P303R2

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 GALNTL6 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 GALNTL6

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

AKR7A2P1,AKR7A3,CACNB2,CDHR3,CPE,CPNE6,DACH1,
DYNC1I2,FLJ46111,GALNT7,GALNTL6,GCM1,GP2,HAO2,
LHFPL1,LRRC49,MACROD2,MC2R,TNNI3K,TPH2,UCN3
ASCL2,C11orf85,C2orf50,C2orf54,CPA6,CSMD3,CYP4F2,
GALNTL6,GLYATL3,KCNF1,KRTAP10-10,LHX1,MCHR1,NTSR1,
PRSS1,SLC7A13,SPANXA2,SPANXC,SPANXD,ABHD11-AS1,WNT3A

AGBL1,ANO7,ATOH1,B3GNT6,LINC00469,LINC00261,CACNA2D2,
CAPN9,CCDC60,CLCA1,FAM174B,GALNTL6,GP9,HEPACAM2,
KLK3,LRRC26,PTGER2,RASD1,REP15,SPINK4,TBC1D2
BPIFB4,CD300LG,CNBD1,CST11,DEFB124,DPYS,DYDC1,
GALNTL6,GLYCAM1,HPN,LIM2,LOC55908,MARCO,NKX6-2,
OR3A4P,REG1A,REG1B,SBSN,SCGB1A1,SCGB3A1,SNORA22
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 GALNTL6


There's no related Drug.
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Cross referenced IDs for GALNTL6
* 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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