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 CSGALNACT1

Basic gene info.	Gene symbol	CSGALNACT1
	Gene name	chondroitin sulfate N-acetylgalactosaminyltransferase 1
	Synonyms	CSGalNAcT-1\|ChGn\|beta4GalNAcT
	Cytomap	UCSC genome browser: 8p21.3
	Genomic location	chr8 :19261671-19540094
	Type of gene	protein-coding
	RefGenes	NM_001130518.1, NM_018371.4,NR_024040.1,
	Ensembl id	ENSG00000147408
	Description	beta4GalNAcT-1chondroitin beta-1,4-N-acetylgalactosaminyltransferase 1chondroitin beta1,4 N-acetylgalactosaminyltransferase
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000147408
	HPRD : 13114
	Vega : OTTHUMG00000130827
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CSGALNACT1
	BioGPS: 55790
	Gene Expression Atlas: ENSG00000147408
	The Human Protein Atlas: ENSG00000147408
Pathway	NCI Pathway Interaction Database: CSGALNACT1
	KEGG: CSGALNACT1
	REACTOME: CSGALNACT1
	ConsensusPathDB
	Pathway Commons: CSGALNACT1
Metabolism	MetaCyc: CSGALNACT1
	HUMANCyc: CSGALNACT1
Regulation	Ensembl's Regulation: ENSG00000147408
	miRBase: chr8 :19,261,671-19,540,094
	TargetScan: NM_001130518
	cisRED: ENSG00000147408
Context	iHOP: CSGALNACT1
	cancer metabolism search in PubMed: CSGALNACT1
	UCL Cancer Institute: CSGALNACT1
Assigned class in ccmGDB	C

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Phenotypic Information for CSGALNACT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CSGALNACT1
	Familial Cancer Database: CSGALNACT1

* 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: CSGALNACT1
	MedGen: CSGALNACT1 (Human Medical Genetics with Condition)
	ClinVar: CSGALNACT1
Phenotype	MGI: CSGALNACT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CSGALNACT1

Mutations for CSGALNACT1

* 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

There's no inter-chromosomal structural variation.

- 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	CSGALNACT1	chr8	19314788	19314808	CSGALNACT1	chr8	19314912	19314932
ovary	CSGALNACT1	chr8	19533956	19533976	CSGALNACT1	chr8	19536386	19536406

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 CSGALNACT1 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
DB148679	COPG2	1	411	7	130301920	130353577	CSGALNACT1	407	513	8	19315938	19316044
DW420626	CSGALNACT1	17	84	8	19589501	19589568	CSGALNACT1	83	300	8	19591592	19591809
N52914	CSGALNACT1	1	167	8	19300761	19300961	LARGE	152	586	22	33790310	33790740
CV347923	CSGALNACT1	1	157	8	19513474	19513629	RNF144B	144	163	6	18439868	18439887

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

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=50)	Stat. for Synonymous SNVs (# total SNVs=20)

Stat. for Deletions (# total SNVs=2)	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
chr8:19316132-19316132	p.D219G	4
chr8:19363277-19363277	p.C23*	2
chr8:19297442-19297443	p.?	2
chr8:19277979-19277979	p.S335Y	2
chr8:19263452-19263452	p.R480C	2
chr8:19363229-19363229	p.D39D	2
chr8:19316028-19316028	p.E254K	1
chr8:19363035-19363035	p.A104V	1
chr8:19266161-19266161	p.G424G	1
chr8:19276254-19276254	p.K380N	1

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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	1	2	1	11			5	1	4			7	5	1	1	1	7	12	1	13
# mutation	1	2	1	9			5	1	4			12	5	1	1	1	7	13	1	14
nonsynonymous SNV		1	1	4			2		3			10	3	1	1	1	5	11		13
synonymous SNV	1	1		5			3	1	1			2	2				2	2	1	1

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
chr8:19316132	p.D219G,CSGALNACT1	4
chr8:19277950	p.L239L,CSGALNACT1	2
chr8:19316071	p.H399N,CSGALNACT1	2
chr8:19277979	p.G212V,CSGALNACT1	2
chr8:19316153	p.R480C,CSGALNACT1	2
chr8:19263452	p.R345S,CSGALNACT1	2
chr8:19363042	p.S335F,CSGALNACT1	2
chr8:19276199	p.D102N,CSGALNACT1	2
chr8:19362961	p.I266I,CSGALNACT1	1
chr8:19277935	p.I184T,CSGALNACT1	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 CSGALNACT1 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 CSGALNACT1

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


ANTXR2,ARNTL2,CASP10,CCNYL1,CSGALNACT1,DSE,FYN, GLIPR1,INTS10,KCTD12,LPCAT2,LSAMP,LUZP1,MCTP2, NRP1,PALMD,PDE10A,PDE4D,RBMS1,SERPINB8,SGK1	AKT3,BMX,C4orf3,CASP10,CLIC2,CLIC4,CSGALNACT1, CXCL12,DPYD,EMCN,FGL2,IL33,LOC145820,OMD, PLCXD3,SGMS1,SKAP2,SLC46A3,TAL1,TFPI,TLL1

ARHGAP31,ASAH1,ATP8B2,BASP1,CDYL2,CSGALNACT1,CTSB, FAM101B,FKBP7,FN1,GPR176,HHIPL1,LAMA4,LAMC1, NTNG2,PCDHGA12,SGTB,TCF4,TXNDC15,WIPF1,ZNF521	AVPR2,CSGALNACT1,F8,FAM13C,GAS1,GLT8D2,HTRA1, JAM2,LDB2,LHFP,LOC285548,LPHN2,OLFML3,PDGFC, RAPGEF4,RECK,SNCAIP,TEK,TGFBR2,TIMP2,ZNF521

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 CSGALNACT1

There's no related Drug.

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Cross referenced IDs for CSGALNACT1

* 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