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 CSGALNACT2

Basic gene info.	Gene symbol	CSGALNACT2
	Gene name	chondroitin sulfate N-acetylgalactosaminyltransferase 2
	Synonyms	CHGN2\|GALNACT-2\|GALNACT2
	Cytomap	UCSC genome browser: 10q11.21
	Genomic location	chr10 :43633933-43680749
	Type of gene	protein-coding
	RefGenes	NM_018590.4,
	Ensembl id	ENSG00000169826
	Description	beta 4 GalNAcT-2chondroitin beta1,4 N-acetylgalactosaminyltransferase 2
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000169826
	HPRD : 11348
	Vega : OTTHUMG00000018023
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CSGALNACT2
	BioGPS: 55454
	Gene Expression Atlas: ENSG00000169826
	The Human Protein Atlas: ENSG00000169826
Pathway	NCI Pathway Interaction Database: CSGALNACT2
	KEGG: CSGALNACT2
	REACTOME: CSGALNACT2
	ConsensusPathDB
	Pathway Commons: CSGALNACT2
Metabolism	MetaCyc: CSGALNACT2
	HUMANCyc: CSGALNACT2
Regulation	Ensembl's Regulation: ENSG00000169826
	miRBase: chr10 :43,633,933-43,680,749
	TargetScan: NM_018590
	cisRED: ENSG00000169826
Context	iHOP: CSGALNACT2
	cancer metabolism search in PubMed: CSGALNACT2
	UCL Cancer Institute: CSGALNACT2
Assigned class in ccmGDB	C

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Phenotypic Information for CSGALNACT2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CSGALNACT2
	Familial Cancer Database: CSGALNACT2

* 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_CARBOHYDRATES

Others
OMIM
Orphanet
Disease	KEGG Disease: CSGALNACT2
	MedGen: CSGALNACT2 (Human Medical Genetics with Condition)
	ClinVar: CSGALNACT2
Phenotype	MGI: CSGALNACT2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CSGALNACT2

Mutations for CSGALNACT2

* 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 CSGALNACT2 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
DA381927	CSGALNACT2	1	396	10	43651063	43654362	ACKR3	397	552	2	237478468	237489138
CN418454	CSGALNACT2	1	143	10	43633949	43650420	PDXDC1	142	599	16	15227443	15228118
BQ637932	CSGALNACT2	1	537	10	43650609	43651145	CDR2	534	621	16	22357678	22357765

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=8

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=65)	Stat. for Synonymous SNVs (# total SNVs=17)

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
chr10:43659419-43659419	p.L362F	8
chr10:43659338-43659338	p.T335T	4
chr10:43654172-43654172	p.R224H	3
chr10:43678796-43678796	p.P479S	3
chr10:43651251-43651251	p.F218F	3
chr10:43662538-43662538	p.Q416K	2
chr10:43650762-43650762	p.E55D	2
chr10:43659339-43659339	p.L336V	2
chr10:43678849-43678849	p.P496P	2
chr10:43651233-43651233	p.I212M	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	2	2		8			4		3	2		11	3	1			7	3	3	12
# mutation	2	2		9			4		3	2		14	3	1			10	3	3	14
nonsynonymous SNV	1	2		8			3		3	1		11	3	1			4	2	1	10
synonymous SNV	1			1			1			1		3					6	1	2	4

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
chr10:43654172	p.R224L	2
chr10:43654238	p.R246T	2
chr10:43662538	p.P496P	2
chr10:43651086	p.Q416K	2
chr10:43678849	p.L163L	2
chr10:43650712	p.V47I	1
chr10:43655966	p.E169G	1
chr10:43650986	p.T335T	1
chr10:43662509	p.G447V	1
chr10:43678742	p.E55E	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 CSGALNACT2 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 CSGALNACT2

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


BACH1,BICC1,CLIC4,CSGALNACT2,DDX21,DSE,FERMT2, FUT11,ITGB1,KCTD20,LATS2,LIMS1,LOX,MAP3K2, PLXNC1,QKI,RIF1,RRAGC,SEC23A,SGTB,ZNF699	ACAP2,ACTR2,ATP11C,BNIP2,CCDC88A,CDC27,CEP170, CSGALNACT2,EEA1,EXOC5,GNA13,KIAA1033,BLOC1S6,RAB8B, RBMS1,RECQL,SGMS1,SGTB,SOCS4,SYNJ1,TMX3

VSTM4,C1S,CSGALNACT2,DZIP1,ENTPD1,EVC,FSTL1, GAS7,GNB4,GPC6,LUM,MAF,MCC,NR3C1, PDGFRB,PKD2,QKI,SULF1,TCF4,ZEB2,ZNF521	CALU,CEP170,CHN1,CSGALNACT2,DENND5A,ELOVL5,FKBP14, GPR155,HECTD2,KCNE4,SLC9B2,PITPNB,PRKD3,QKI, RAB11FIP2,RBMS1,RHOQ,SLC39A6,TBCEL,TCEAL4,TCF4

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 CSGALNACT2

There's no related Drug.

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Cross referenced IDs for CSGALNACT2

* 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