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 GALNT13

Basic gene info.	Gene symbol	GALNT13
	Gene name	polypeptide N-acetylgalactosaminyltransferase 13
	Synonyms	GalNAc-T13
	Cytomap	UCSC genome browser: 2q24.1
	Genomic location	chr2 :154728425-155310489
	Type of gene	protein-coding
	RefGenes	NM_001301627.1, NM_052917.3,
	Ensembl id	ENSG00000144278
	Description	GalNAc transferase 13UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 13UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)polypeptide GalNAc transferase 13pp-GaNTase 13protein-UDP acetylgalactosam
	Modification date	20141207
dbXrefs	MIM : 608369
	HGNC : HGNC
	Ensembl : ENSG00000144278
	HPRD : 16325
	Vega : OTTHUMG00000131917
Protein	UniProt: Q8IUC8 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GALNT13
	BioGPS: 114805
	Gene Expression Atlas: ENSG00000144278
	The Human Protein Atlas: ENSG00000144278
Pathway	NCI Pathway Interaction Database: GALNT13
	KEGG: GALNT13
	REACTOME: GALNT13
	ConsensusPathDB
	Pathway Commons: GALNT13
Metabolism	MetaCyc: GALNT13
	HUMANCyc: GALNT13
Regulation	Ensembl's Regulation: ENSG00000144278
	miRBase: chr2 :154,728,425-155,310,489
	TargetScan: NM_001301627
	cisRED: ENSG00000144278
Context	iHOP: GALNT13
	cancer metabolism search in PubMed: GALNT13
	UCL Cancer Institute: GALNT13
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for GALNT13(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GALNT13
	Familial Cancer Database: GALNT13

* 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	608369; gene.
Orphanet
Disease	KEGG Disease: GALNT13
	MedGen: GALNT13 (Human Medical Genetics with Condition)
	ClinVar: GALNT13
Phenotype	MGI: GALNT13 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GALNT13

Mutations for GALNT13

* 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
liver	GALNT13	chr2	155281309	155281309		chr10	29233283	29233283
ovary	GALNT13	chr2	154792030	154792050	GALNT13	chr2	154795397	154795417
ovary	GALNT13	chr2	154897514	154897534	GALNT13	chr2	154929979	154929999
ovary	GALNT13	chr2	154898956	154898976	GALNT13	chr2	154899103	154899123
ovary	GALNT13	chr2	155060396	155060416	GALNT13	chr2	155225724	155225744
ovary	GALNT13	chr2	155069331	155069351	GALNT13	chr2	155069561	155069581
ovary	GALNT13	chr2	155154989	155155189	GALNT13	chr2	155155282	155155482
ovary	GALNT13	chr2	155155018	155155038	GALNT13	chr2	155155421	155155441
ovary	GALNT13	chr2	155199393	155199413	GALNT13	chr2	155201245	155201265
ovary	GALNT13	chr2	155203494	155203514	GALNT13	chr2	155200879	155200899
ovary	GALNT13	chr2	155280058	155280078	GALNT13	chr2	155282761	155282781
pancreas	GALNT13	chr2	155200929	155200949	GALNT13	chr2	155200866	155200886

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 GALNT13 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
BM931973	AKAP9	160	333	7	91725929	91726102	GALNT13	319	338	2	155004397	155004416
Z97017	GALNT13	1	1585	2	155153258	155154839	USP34	1585	1748	2	61479516	61479679
DW462544	GALNT13	17	219	2	155100531	155100733	GALNT13	218	368	2	155099822	155099972
BF665493	PRKCA	1	387	17	64511411	64511798	GALNT13	368	394	2	154989282	154989308

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	2		2	3		5		4		1					1	1
GAIN (# sample)	1	2		1	3				1		1					1	1
LOSS (# sample)				1			5		3

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=147)	Stat. for Synonymous SNVs (# total SNVs=29)

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
chr2:155102455-155102455	p.E273*	4
chr2:155098678-155098678	p.E149D	4
chr2:155157982-155157982	p.R346W	4
chr2:155158006-155158006	p.P354S	3
chr2:155098590-155098590	p.V120A	3
chr2:155295140-155295140	p.D478N	3
chr2:155102432-155102432	p.R265H	3
chr2:155099239-155099239	p.Y169Y	2
chr2:155158078-155158078	p.D378Y	2
chr2:155099275-155099275	p.R181S	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=3

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	1	2		17	3		5		5			19	15	4		1	28	10		12
# mutation	1	2		19	3		6		5			26	15	4		1	32	10		15
nonsynonymous SNV	1	2		14	2		5		3			24	12	3			23	7		12
synonymous SNV				5	1		1		2			2	3	1		1	9	3		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
chr2:155158006	p.P354S	3
chr2:155158018	p.R476Q	2
chr2:155102432	p.R265H	2
chr2:155099233	p.E167E	2
chr2:155099239	p.Y169Y	2
chr2:154801126	p.L487F	2
chr2:155295135	p.E39G	2
chr2:155115588	p.G358C	2
chr2:155295167	p.E304D	2
chr2:155115593	p.G306E	2

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 GALNT13 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 GALNT13

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


CHRM3,FLJ23867,FOXC1,FZD7,GALNT13,GLP1R,ITGA6, KCNN4,KCNS1,LPO,MFI2,MIA,PDIA2,PRR4, PTH2R,SMR3A,SMR3B,SOX10,SOX6,TMEM74,TMX4	AKAP12,CLMP,MTURN,DDHD2,DOCK11,EHBP1,EPB41L2, FAM92A1,GALNT13,GCOM1,GLYAT,ITSN1,MARK1,NMT2, PALM2-AKAP2,PALMD,PCDH9,PYGL,SAR1A,SEPT11,STX7

BEX1,C11orf16,LINC00523,CACNA1I,CD8B,CYMP,DKK4, DPT,DSCR10,EPHA8,FER1L5,GALNT13,KRTAP19-8,LECT1, MAGEB10,MAGEB2,MBD3L1,C7orf62,MOG,NELL1,RBP3	ANO3,ATCAY,ATP2B2,DIRAS2,ECM2,FGF14,FZD7, GALNT13,GARNL3,GRIA2,HMP19,HS6ST3,NAPB,NDRG4, PHOX2B,PPP2R2C,PRIMA1,SYT1,SYT5,SYT9,TPPP3

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 GALNT13

There's no related Drug.

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Cross referenced IDs for GALNT13

* 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