Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 GALNT11

Basic gene info.	Gene symbol	GALNT11
	Gene name	polypeptide N-acetylgalactosaminyltransferase 11
	Synonyms	GALNACT11
	Cytomap	UCSC genome browser: 7q36.1\|7q36.1
	Genomic location	chr7 :151722777-151819427
	Type of gene	protein-coding
	RefGenes	NM_022087.2,
	Ensembl id	ENSG00000178234
	Description	GALNAC-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 date	20141207
dbXrefs	MIM : 615130
	HGNC : HGNC
	Ensembl : ENSG00000178234
	HPRD : 13560
	Vega : OTTHUMG00000157251
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GALNT11
	BioGPS: 63917
	Gene Expression Atlas: ENSG00000178234
	The Human Protein Atlas: ENSG00000178234
Pathway	NCI Pathway Interaction Database: GALNT11
	KEGG: GALNT11
	REACTOME: GALNT11
	ConsensusPathDB
	Pathway Commons: GALNT11
Metabolism	MetaCyc: GALNT11
	HUMANCyc: GALNT11
Regulation	Ensembl's Regulation: ENSG00000178234
	miRBase: chr7 :151,722,777-151,819,427
	TargetScan: NM_022087
	cisRED: ENSG00000178234
Context	iHOP: GALNT11
	cancer metabolism search in PubMed: GALNT11
	UCL Cancer Institute: GALNT11
Assigned class in ccmGDB	C

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Phenotypic Information for GALNT11(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: GALNT11
	MedGen: GALNT11 (Human Medical Genetics with Condition)
	ClinVar: GALNT11
Phenotype	MGI: GALNT11 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	GALNT11	chr7	151768064	151768264		chr7	154943358	154943558
ovary	GALNT11	chr7	151768234	151768434		chr12	131326147	131326347
ovary	GALNT11	chr7	151782393	151782413	MLL3	chr7	151900500	151900520
ovary	GALNT11	chr7	151798151	151798171	GALNT11	chr7	151798756	151798776
ovary	GALNT11	chr7	151817187	151817207	GALNT11	chr7	151806369	151806389
pancreas	GALNT11	chr7	151768324	151768344	MLL3	chr7	152049251	152049271

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GALNT11 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BE169979	GALNT11	38	116	7	151805264	151805342	GALNT11	109	632	7	151805341	151814460
AA776153	KIF1B	1	259	1	10440888	10441146	GALNT11	253	434	7	151810452	151814393

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID	brca	cns	cerv	endome	haematopo	kidn	Lintest	liver	lung	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	2	2	1						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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr7:151818003-151818003	p.R549W	3
chr7:151810418-151810418	p.E390K	3
chr7:151807728-151807728	p.R360W	2
chr7:151791477-151791477	p.F55L	2
chr7:151802408-151802408	p.R222H	2
chr7:151802422-151802422	p.R227*	2
chr7:151791543-151791543	p.D77D	2
chr7:151800307-151800307	p.R177H	2
chr7:151805252-151805252	p.T281M	1
chr7:151791456-151791456	p.H48H	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2	4		6	1		1		3	1		5	2			2	7	7		9
# mutation	2	4		7	1		1		3	1		6	2			2	8	8		11
nonsynonymous SNV	1	4		5	1		1		3	1		4	2			2	3	3		9
synonymous SNV	1			2								2					5	5		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr7:151791477	p.F55F	2
chr7:151810418	p.E390K	2
chr7:151807728	p.R360W	2
chr7:151810346	p.R222H	1
chr7:151791456	p.I371I	1
chr7:151815816	p.M593I	1
chr7:151800240	p.G49R	1
chr7:151805279	p.Q256E	1
chr7:151810363	p.R381R	1
chr7:151791457	p.S600C	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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