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 GALNT11
Basic gene info.Gene symbolGALNT11
Gene namepolypeptide N-acetylgalactosaminyltransferase 11
SynonymsGALNACT11
CytomapUCSC genome browser: 7q36.1|7q36.1
Genomic locationchr7 :151722777-151819427
Type of geneprotein-coding
RefGenesNM_022087.2,
Ensembl idENSG00000178234
DescriptionGALNAC-T11UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 11UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)polypeptide GalNAc transferase 11pp-GaNTase 11protein-UDP acetylgalactosaminyltransfe
Modification date20141207
dbXrefs MIM : 615130
HGNC : HGNC
Ensembl : ENSG00000178234
HPRD : 13560
Vega : OTTHUMG00000157251
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALNT11
BioGPS: 63917
Gene Expression Atlas: ENSG00000178234
The Human Protein Atlas: ENSG00000178234
PathwayNCI Pathway Interaction Database: GALNT11
KEGG: GALNT11
REACTOME: GALNT11
ConsensusPathDB
Pathway Commons: GALNT11
MetabolismMetaCyc: GALNT11
HUMANCyc: GALNT11
RegulationEnsembl's Regulation: ENSG00000178234
miRBase: chr7 :151,722,777-151,819,427
TargetScan: NM_022087
cisRED: ENSG00000178234
ContextiHOP: GALNT11
cancer metabolism search in PubMed: GALNT11
UCL Cancer Institute: GALNT11
Assigned class in ccmGDBC

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Phenotypic Information for GALNT11(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALNT11
Familial Cancer Database: GALNT11
* 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: GALNT11
MedGen: GALNT11 (Human Medical Genetics with Condition)
ClinVar: GALNT11
PhenotypeMGI: GALNT11 (International Mouse Phenotyping Consortium)
PhenomicDB: GALNT11

Mutations for GALNT11
* 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
ovaryGALNT11chr7151768064151768264chr7154943358154943558
ovaryGALNT11chr7151768234151768434chr12131326147131326347
ovaryGALNT11chr7151782393151782413MLL3chr7151900500151900520
ovaryGALNT11chr7151798151151798171GALNT11chr7151798756151798776
ovaryGALNT11chr7151817187151817207GALNT11chr7151806369151806389
pancreasGALNT11chr7151768324151768344MLL3chr7152049251152049271
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 GALNT11 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE169979GALNT11381167151805264151805342GALNT111096327151805341151814460
AA776153KIF1B125911044088810441146GALNT112534347151810452151814393

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 # sample221     1 1  2  1
GAIN (# sample) 2      1 1  2  1
LOSS (# sample)2 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=48)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr7:151810418-151810418p.E390K3
chr7:151818003-151818003p.R549W3
chr7:151800307-151800307p.R177H2
chr7:151807728-151807728p.R360W2
chr7:151791477-151791477p.F55L2
chr7:151802408-151802408p.R222H2
chr7:151802422-151802422p.R227*2
chr7:151791543-151791543p.D77D2
chr7:151791435-151791435p.P41P1
chr7:151805245-151805245p.A279T1

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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
# sample24 61 1 31 52  277 9
# mutation24 71 1 31 62  288 11
nonsynonymous SNV14 51 1 31 42  233 9
synonymous SNV1  2       2    55 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
chr7:151807728p.R360W2
chr7:151791477p.F55F2
chr7:151810418p.E390K2
chr7:151805245p.D125D1
chr7:151791434p.R291R1
chr7:151798006p.R482L1
chr7:151815785p.R126C1
chr7:151805265p.G292R1
chr7:151791456p.R484R1
chr7:151810346p.A140V1

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 GALNT11 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 GALNT11

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

AGK,BDNF-AS,CUL1,GALNT11,GTF2IP1,KCTD7,KRBA1,
LOC100302640,LUC7L2,MKRN1,PMPCB,PRKAG2,REPIN1,TMEM168,
WDR60,ZNF212,ZNF282,ZNF746,ZNF767P,ZNF786,ZNF862
BACE1,BLMH,XXYLT1,FAM225A,FAM225B,CAMKK2,CIAO1,
DCTD,DMBT1,EXT2,FAM171A1,GALNT11,GALNT16,HDAC8,
HEXA,KCTD18,NT5DC2,PTPRA,SH3GL3,TXNRD3NB,VPS26B

ACTR3B,AGK,APLF,COPG2,CRCP,CROT,CUL1,
EXOC4,GALNT11,LMBR1,MEST,SRPK2,TMEM150A,TRIM4,
CEP41,TSPAN33,TYW1,ZNF212,ZNF746,ZNF786,ZSCAN21
C15orf41,CNRIP1,ETNK2,F8,FAM13C,FAM171B,GALNT11,
GLT8D2,GPR1,JAM2,LHFP,LUM,PABPC5,PLS3,
QKI,RECK,RHOJ,TAF9B,TCTN1,TGFBR2,ZDBF2
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 GALNT11


There's no related Drug.
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Cross referenced IDs for GALNT11
* 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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