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 GALNTL6

Basic gene info.	Gene symbol	GALNTL6
	Gene name	polypeptide N-acetylgalactosaminyltransferase-like 6
	Synonyms	GALNACT20\|GALNT17\|GalNAc-T6L
	Cytomap	UCSC genome browser: 4q34.1
	Genomic location	chr4 :172734574-173961558
	Type of gene	protein-coding
	RefGenes	NM_001034845.2,
	Ensembl id	ENSG00000174473
	Description	GaNTase 17GalNAc transferase 17UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 17UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 20UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransfera
	Modification date	20141207
dbXrefs	MIM : 615138
	HGNC : HGNC
Protein	UniProt: Q49A17 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GALNTL6
	BioGPS: 442117
	Gene Expression Atlas: ENSG00000174473
	The Human Protein Atlas: ENSG00000174473
Pathway	NCI Pathway Interaction Database: GALNTL6
	KEGG: GALNTL6
	REACTOME: GALNTL6
	ConsensusPathDB
	Pathway Commons: GALNTL6
Metabolism	MetaCyc: GALNTL6
	HUMANCyc: GALNTL6
Regulation	Ensembl's Regulation: ENSG00000174473
	miRBase: chr4 :172,734,574-173,961,558
	TargetScan: NM_001034845
	cisRED: ENSG00000174473
Context	iHOP: GALNTL6
	cancer metabolism search in PubMed: GALNTL6
	UCL Cancer Institute: GALNTL6
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for GALNTL6(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GALNTL6
	Familial Cancer Database: GALNTL6

* 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: GALNTL6
	MedGen: GALNTL6 (Human Medical Genetics with Condition)
	ClinVar: GALNTL6
Phenotype	MGI: GALNTL6 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GALNTL6

Mutations for GALNTL6

* 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	GALNTL6	chr4	173360321	173360341	ODZ3	chr4	183552344	183552364
pancreas	GALNTL6	chr4	172826170	172826370	TMEM117	chr12	44302122	44302322
pancreas	GALNTL6	chr4	173159682	173159702	RWDD4	chr4	184577119	184577139
pancreas	GALNTL6	chr4	173332792	173332812	GALNTL6	chr4	173332843	173332863
pancreas	GALNTL6	chr4	173476128	173476148	GALNTL6	chr4	173446207	173446227
pancreas	GALNTL6	chr4	173515480	173515500		chr11	127818586	127818606
pancreas	GALNTL6	chr4	173723968	173723988	GALNTL6	chr4	173833423	173833443
prostate	GALNTL6	chr4	173233547	173233547	GALNTL6	chr4	173539655	173539655
skin	GALNTL6	chr4	173631903	173631903	GALNTL6	chr4	173632747	173632747

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 GALNTL6 related fusion information.

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

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

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=79)	Stat. for Synonymous SNVs (# total SNVs=22)

Stat. for Deletions (# total SNVs=4)	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
chr4:173930333-173930333	p.R459Q	3
chr4:173961139-173961141	p.K567delK	3
chr4:173232893-173232893	p.R126C	3
chr4:173269816-173269816	p.L177I	2
chr4:173873377-173873377	p.P447T	2
chr4:173232810-173232810	p.H98R	2
chr4:172735787-172735787	p.L19S	2
chr4:173269761-173269761	p.R158R	2
chr4:173730571-173730571	p.R205S	2
chr4:173730671-173730671	p.N238S	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	4	2	2	13			5		1	1	1	17	5	1			17	12		11
# mutation	4	2	2	13			5		1	1	1	18	5	1			16	14		13
nonsynonymous SNV	3		1	12			5		1	1	1	12	4				12	12		11
synonymous SNV	1	2	1	1								6	1	1			4	2		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
chr4:173930333	p.R459Q	3
chr4:173232893	p.R403W	2
chr4:172735864	p.M1V	2
chr4:173269816	p.L64F	2
chr4:172735764	p.L177I	2
chr4:173150860	p.M11I	2
chr4:173852374	p.P303R	2
chr4:173734859	p.R126C	2
chr4:173873245	p.P446L	2
chr4:172735732	p.Q45E	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 GALNTL6 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 GALNTL6

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


AKR7A2P1,AKR7A3,CACNB2,CDHR3,CPE,CPNE6,DACH1, DYNC1I2,FLJ46111,GALNT7,GALNTL6,GCM1,GP2,HAO2, LHFPL1,LRRC49,MACROD2,MC2R,TNNI3K,TPH2,UCN3	ASCL2,C11orf85,C2orf50,C2orf54,CPA6,CSMD3,CYP4F2, GALNTL6,GLYATL3,KCNF1,KRTAP10-10,LHX1,MCHR1,NTSR1, PRSS1,SLC7A13,SPANXA2,SPANXC,SPANXD,ABHD11-AS1,WNT3A

AGBL1,ANO7,ATOH1,B3GNT6,LINC00469,LINC00261,CACNA2D2, CAPN9,CCDC60,CLCA1,FAM174B,GALNTL6,GP9,HEPACAM2, KLK3,LRRC26,PTGER2,RASD1,REP15,SPINK4,TBC1D2	BPIFB4,CD300LG,CNBD1,CST11,DEFB124,DPYS,DYDC1, GALNTL6,GLYCAM1,HPN,LIM2,LOC55908,MARCO,NKX6-2, OR3A4P,REG1A,REG1B,SBSN,SCGB1A1,SCGB3A1,SNORA22

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 GALNTL6

There's no related Drug.

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Cross referenced IDs for GALNTL6

* 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