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 GALNT10

Basic gene info.	Gene symbol	GALNT10
	Gene name	polypeptide N-acetylgalactosaminyltransferase 10
	Synonyms	GALNACT10\|PPGALNACT10\|PPGANTASE10
	Cytomap	UCSC genome browser: 5q33.2
	Genomic location	chr5 :153570294-153800543
	Type of gene	protein-coding
	RefGenes	NM_198321.3, NM_017540.3,NM_024564.1,
	Ensembl id	ENSG00000164574
	Description	GalNAc transferase 10UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 10UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)
	Modification date	20141207
dbXrefs	MIM : 608043
	HGNC : HGNC
	Ensembl : ENSG00000164574
	HPRD : 12157
	Vega : OTTHUMG00000130145
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GALNT10
	BioGPS: 55568
	Gene Expression Atlas: ENSG00000164574
	The Human Protein Atlas: ENSG00000164574
Pathway	NCI Pathway Interaction Database: GALNT10
	KEGG: GALNT10
	REACTOME: GALNT10
	ConsensusPathDB
	Pathway Commons: GALNT10
Metabolism	MetaCyc: GALNT10
	HUMANCyc: GALNT10
Regulation	Ensembl's Regulation: ENSG00000164574
	miRBase: chr5 :153,570,294-153,800,543
	TargetScan: NM_198321
	cisRED: ENSG00000164574
Context	iHOP: GALNT10
	cancer metabolism search in PubMed: GALNT10
	UCL Cancer Institute: GALNT10
Assigned class in ccmGDB	C

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Phenotypic Information for GALNT10(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GALNT10
	Familial Cancer Database: GALNT10

* 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: GALNT10
	MedGen: GALNT10 (Human Medical Genetics with Condition)
	ClinVar: GALNT10
Phenotype	MGI: GALNT10 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GALNT10

Mutations for GALNT10

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	GALNT10	chr5	153763540	153763540		chr12	71462294	71462294
ovary	GALNT10	chr5	153766697	153766717		chr19	11498835	11498855
ovary	GALNT10	chr5	153766815	153766835		chr5	154696202	154696222
pancreas	GALNT10	chr5	153658912	153659112	CBL	chr11	119124194	119124394
pancreas	GALNT10	chr5	153666875	153666895		chr5	159343243	159343263

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 GALNT10 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
BF155072	GALNT10	1	116	5	153800378	153800494	GALNT10	117	472	5	153799900	153800255
DA949043	GALNT10	1	305	5	153778005	153778307	MYH9	302	557	22	36707599	36707854

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	1	3					9		4		1		1		1	1
GAIN (# sample)		1					1		3				1		1
LOSS (# sample)	1	2					8		1		1					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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=49)	Stat. for Synonymous SNVs (# total SNVs=18)

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
chr5:153709146-153709146	p.R139H	3
chr5:153755896-153755896	p.R210*	3
chr5:153755919-153755919	p.L217L	2
chr5:153677535-153677535	p.T99T	2
chr5:153760081-153760081	p.Y276Y	2
chr5:153792479-153792479	p.D473H	2
chr5:153789197-153789197	p.A421T	2
chr5:153789216-153789216	p.R427H	2
chr5:153709265-153709265	p.E179K	2
chr5:153760181-153760181	p.D310Y	2

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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	1	10	1		2		3	1		7	3			3	7	8	1	10
# mutation		2	1	9	1		2		3	1		7	3			3	7	8	1	10
nonsynonymous SNV		2		6	1		1		1	1		4	3			2	4	4	1	7
synonymous SNV			1	3			1		2			3				1	3	4		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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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
chr5:153760070	p.I349I	2
chr5:153765981	p.D76N	2
chr5:153674442	p.L217L	2
chr5:153765879	p.D273N	2
chr5:153765888	p.P315P	2
chr5:153755919	p.A318A	2
chr5:153765900	p.F322F	2
chr5:153765930	p.D184G	1
chr5:153709212	p.L332L	1
chr5:153789255	p.R492C	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 GALNT10 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 GALNT10

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


ARHGEF38,ATXN1,BNC2,KIAA0825,CTNNA1,EVC,FAM114A2, FBN1,FYCO1,GALNT10,ARHGAP35,GXYLT2,KIAA0247,LIMA1, LOC100129034,MFAP3,PRICKLE2,RAB27B,SH3D19,SLC24A2,YIPF5	ADAM10,ATRN,C12orf49,CACNA1D,CHST15,EDARADD,GALNT10, LTBP2,MAGI3,MICALCL,MYOF,PTPRJ,RAB27B,RASEF, SEPT8,SFMBT2,SIPA1L1,SLC2A10,TTC26,TXLNA,WWC3

ACVR1,AFF4,ARHGAP26,CTNNA1,ECM1,EPAS1,GALNT10, GALNT2,CEMIP,KIF26B,LAMB1,LAMC1,MAP4,MAST4, MEGF8,NDST1,SDC3,SH3PXD2A,SH3PXD2B,TGFBI,TNKS1BP1	ABHD2,ACLY,ASCC3,EIF4G1,EPRS,GALNT10,GANAB, MKI67,PDE11A,PRKDC,SBNO1,SEC16A,SEC24C,SEC61A1, SMC1A,STT3A,TAF15,TMEM214,TRIP11,UGGT1,VPS53

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 GALNT10

There's no related Drug.

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Cross referenced IDs for GALNT10

* 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