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 GALNT6

Basic gene info.	Gene symbol	GALNT6
	Gene name	polypeptide N-acetylgalactosaminyltransferase 6
	Synonyms	GALNAC-T6\|GalNAcT6
	Cytomap	UCSC genome browser: 12q13
	Genomic location	chr12 :51745832-51785200
	Type of gene	protein-coding
	RefGenes	NM_007210.3,
	Ensembl id	ENSG00000139629
	Description	GalNAc transferase 6UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 6UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 6UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-
	Modification date	20141207
dbXrefs	MIM : 605148
	HGNC : HGNC
	Ensembl : ENSG00000139629
	HPRD : 05512
	Vega : OTTHUMG00000185181
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GALNT6
	BioGPS: 11226
	Gene Expression Atlas: ENSG00000139629
	The Human Protein Atlas: ENSG00000139629
Pathway	NCI Pathway Interaction Database: GALNT6
	KEGG: GALNT6
	REACTOME: GALNT6
	ConsensusPathDB
	Pathway Commons: GALNT6
Metabolism	MetaCyc: GALNT6
	HUMANCyc: GALNT6
Regulation	Ensembl's Regulation: ENSG00000139629
	miRBase: chr12 :51,745,832-51,785,200
	TargetScan: NM_007210
	cisRED: ENSG00000139629
Context	iHOP: GALNT6
	cancer metabolism search in PubMed: GALNT6
	UCL Cancer Institute: GALNT6
Assigned class in ccmGDB	C

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Phenotypic Information for GALNT6(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GALNT6
	Familial Cancer Database: GALNT6

* 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: GALNT6
	MedGen: GALNT6 (Human Medical Genetics with Condition)
	ClinVar: GALNT6
Phenotype	MGI: GALNT6 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GALNT6

Mutations for GALNT6

* 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 GALNT6 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
AK225124	C3	1	614	19	6714364	6720616	GALNT6	609	2599	12	51747149	51758061
AI909009	GALNT6	15	325	12	51748252	51751944	GALNT6	321	451	12	51747902	51748032

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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=37)	Stat. for Synonymous SNVs (# total SNVs=25)

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
chr12:51773357-51773357	p.K70R	3
chr12:51758021-51758021	p.P311P	3
chr12:51758030-51758030	p.F308F	3
chr12:51749712-51749712	p.R545C	3
chr12:51753078-51753078	p.C402C	2
chr12:51752037-51752037	p.F459F	2
chr12:51759245-51759245	p.Q261Q	2
chr12:51751178-51751178	p.K520fs*79	2
chr12:51773084-51773084	p.R161L	2
chr12:51749711-51749711	p.R545H	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=4

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	4	3		14	1		4		1			9	2	3		1	20	2		4
# mutation	4	3		12	1		4		1			10	2	3		1	27	2		5
nonsynonymous SNV	1			7	1		3					6	2	2		1	17	2		2
synonymous SNV	3	3		5			1		1			4		1			10			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
chr12:51773357	p.K70R	3
chr12:51758021	p.R161L	2
chr12:51758030	p.P311P	2
chr12:51754561	p.F308F	2
chr12:51773084	p.F459F	2
chr12:51752037	p.T371A	2
chr12:51753107	p.V405L	1
chr12:51773181	p.E338E	1
chr12:51757921	p.S199R	1
chr12:51773463	p.C527C	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 GALNT6 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 GALNT6

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


C1orf64,CCDC125,CREB3L4,FBP1,FOXA1,GALNT6,GPR160, INPP5J,LIMA1,PHOSPHO2,PRR15,SLC2A10,SLC44A4,SLC4A8, SPDEF,TCEAL1,TCEAL3,TCEAL6,TRERF1,TRIM3,XBP1	AAGAB,ARSD,ARSG,DLG3,DNAJC12,ERBB3,FOXA1, GALNT6,GOLM1,HHAT,KIAA0319L,LEO1,PRLR,PROM2, RAB11FIP4,SEZ6L2,SLC4A8,SYTL2,VAV3,WNK4,ZYG11A

ACVR1B,APCDD1,AXIN2,CEACAM6,GALNT6,GUCY2C,ILDR1, KRT23,MANSC1,MUC20,MYO1D,PRR15,REPS2,SAMD12, SCARB1,SEMA5A,SLC4A8,SORL1,VWA2,WWP1,ZNF704	AQP3,CCDC108,CD82,CYP2J2,DAK,DNASE1,EMB, GALNT6,KCNH6,LOC647121,MGAT3,MLXIPL,MST1,PFKFB4, PLB1,RBP3,SERPINA1,SI,SLC28A2,TMEM92,ZNF488

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 GALNT6

There's no related Drug.

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Cross referenced IDs for GALNT6

* 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