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 GALNT2

Basic gene info.	Gene symbol	GALNT2
	Gene name	polypeptide N-acetylgalactosaminyltransferase 2
	Synonyms	GalNAc-T2
	Cytomap	UCSC genome browser: 1q41-q42
	Genomic location	chr1 :230202955-230417875
	Type of gene	protein-coding
	RefGenes	NM_001291866.1, NM_004481.4,NR_120373.1,
	Ensembl id	ENSG00000143641
	Description	UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 2UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)polypeptide GalNAc transferase 2pp-GaNTase 2
	Modification date	20141222
dbXrefs	MIM : 602274
	HGNC : HGNC
	Ensembl : ENSG00000143641
	HPRD : 03782
	Vega : OTTHUMG00000037771
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GALNT2
	BioGPS: 2590
	Gene Expression Atlas: ENSG00000143641
	The Human Protein Atlas: ENSG00000143641
Pathway	NCI Pathway Interaction Database: GALNT2
	KEGG: GALNT2
	REACTOME: GALNT2
	ConsensusPathDB
	Pathway Commons: GALNT2
Metabolism	MetaCyc: GALNT2
	HUMANCyc: GALNT2
Regulation	Ensembl's Regulation: ENSG00000143641
	miRBase: chr1 :230,202,955-230,417,875
	TargetScan: NM_001291866
	cisRED: ENSG00000143641
Context	iHOP: GALNT2
	cancer metabolism search in PubMed: GALNT2
	UCL Cancer Institute: GALNT2
Assigned class in ccmGDB	C

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Phenotypic Information for GALNT2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GALNT2
	Familial Cancer Database: GALNT2

* 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: GALNT2
	MedGen: GALNT2 (Human Medical Genetics with Condition)
	ClinVar: GALNT2
Phenotype	MGI: GALNT2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GALNT2

Mutations for GALNT2

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GALNT2 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
BJ995070	ZNF664	1	98	12	124457788	124458467	GALNT2	92	600	1	230416045	230416553
AW015340	GALNT2	11	252	1	230301660	230301899	AUTS2	243	331	7	69722942	69723030
AW992137	GALNT2	1	77	1	230272431	230272507	GALNT2	76	328	1	230305798	230306050
AF130059	SMOC1	15	330	14	70351984	70352299	GALNT2	322	691	1	230415455	230415823
BG985354	GALNT2	27	300	1	230258147	230258423	BRD9	293	507	5	882190	882404
BQ335474	GALNT2	10	280	1	230398716	230410299	MEMO1	274	330	2	32217481	32217537

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

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=58)	Stat. for Synonymous SNVs (# total SNVs=30)

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
chr1:230398367-230398367	p.F395L	3
chr1:230372444-230372444	p.R194*	3
chr1:230386265-230386265	p.K323R	2
chr1:230314000-230314000	p.D55H	2
chr1:230415081-230415081	p.L531L	2
chr1:230398658-230398658	p.?	2
chr1:230398700-230398700	p.L421P	2
chr1:230338999-230338999	p.R113*	2
chr1:230401027-230401027	p.Q452*	2
chr1:230372463-230372463	p.R200Q	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	3	4	1	12	1		4		2	2	1	13	1	2		1	5	3		10
# mutation	3	4	1	13	1		4		2	2	1	13	1	2		1	5	3		13
nonsynonymous SNV	2	1		10	1		3			1	1	6	1	1			3	3		8
synonymous SNV	1	3	1	3			1		2	1		7		1		1	2			5

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
chr1:230398367	p.K285R,GALNT2	2
chr1:230386265	p.R84R,GALNT2	2
chr1:230415081	p.L493L,GALNT2	2
chr1:230381875	p.A228T,GALNT2	2
chr1:230339028	p.F357L,GALNT2	2
chr1:230371838	p.N239S,GALNT2	1
chr1:230391063	p.R380R,GALNT2	1
chr1:230401027	p.E25Q,GALNT2	1
chr1:230379172	p.K151T,GALNT2	1
chr1:230314024	p.Y246C,GALNT2	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 GALNT2 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 GALNT2

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


ADAM23,AVPI1,C1R,LINC00473,CAPN2,ECEL1,EXTL3, FNDC3B,FNDC4,GALNT2,COLGALT1,GRAMD1B,H6PD,MCTP2, PLOD3,PLXNA1,RAB4A,SNAP47,SYDE1,TAF5L,TNFRSF1A	AARS,AP2A1,B4GALT2,C1orf216,DCTN1,EHD1,GALNT2, ITFG3,LAMB2,LRP3,MXD4,NUCB1,PKN1,PLXND1, POR,RNPEPL1,RPS6KA4,ST3GAL2,TMEM104,USF2,ZBED1

ARAP3,ARHGEF11,ATF6,BCL9,CGNL1,GALNT2,GLUL, GYLTL1B,IGF2,LAMA5,LRP1,MYO10,NCSTN,PI4KB, PIK3C2B,SETDB1,SHC1,STRA6,STX6,TAF5L,ZNF687	AARS,ABCC1,LINC00346,CBX2,CLSTN3,DOC2B,ENG, GALNT2,HK1,LRRC37A3,MAP3K6,MAPK11,MMRN2,PLXND1, SELP,SLC43A3,SRP68,STAT5A,TNFRSF8,TXLNA,VCP

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 GALNT2

There's no related Drug.

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Cross referenced IDs for GALNT2

* 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