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 C1GALT1C1

Basic gene info.	Gene symbol	C1GALT1C1
	Gene name	C1GALT1-specific chaperone 1
	Synonyms	C1GALT2\|C38H2-L1\|COSMC\|MST143\|TNPS
	Cytomap	UCSC genome browser: Xq24
	Genomic location	chrX :119759528-119764005
	Type of gene	protein-coding
	RefGenes	NM_001011551.2, NM_152692.4,
	Ensembl id	ENSG00000171155
	Description	C1Gal-T2C38H2-like protein 1beta 1,3-galactosyltransferase 2core 1 beta1,3-galactosyltransferase 2core 1 beta3-Gal-T2core 1 beta3-galactosyltransferase-specific molecular chaperone
	Modification date	20141207
dbXrefs	MIM : 300611
	HGNC : HGNC
	Ensembl : ENSG00000171155
	HPRD : 06462
	Vega : OTTHUMG00000022305
Protein	UniProt: Q96EU7 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_C1GALT1C1
	BioGPS: 29071
	Gene Expression Atlas: ENSG00000171155
	The Human Protein Atlas: ENSG00000171155
Pathway	NCI Pathway Interaction Database: C1GALT1C1
	KEGG: C1GALT1C1
	REACTOME: C1GALT1C1
	ConsensusPathDB
	Pathway Commons: C1GALT1C1
Metabolism	MetaCyc: C1GALT1C1
	HUMANCyc: C1GALT1C1
Regulation	Ensembl's Regulation: ENSG00000171155
	miRBase: chrX :119,759,528-119,764,005
	TargetScan: NM_001011551
	cisRED: ENSG00000171155
Context	iHOP: C1GALT1C1
	cancer metabolism search in PubMed: C1GALT1C1
	UCL Cancer Institute: C1GALT1C1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for C1GALT1C1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: C1GALT1C1
	Familial Cancer Database: C1GALT1C1

* 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	300611; gene. 300622; phenotype.
Orphanet
Disease	KEGG Disease: C1GALT1C1
	MedGen: C1GALT1C1 (Human Medical Genetics with Condition)
	ClinVar: C1GALT1C1
Phenotype	MGI: C1GALT1C1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: C1GALT1C1

Mutations for C1GALT1C1

* 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 C1GALT1C1 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

T10800

C1GALT1C1

119760593

119760648

C1GALT1C1

177

119760501

119760634

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

There's no copy number variation information in COSMIC data for this gene.

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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=21)	Stat. for Synonymous SNVs (# total SNVs=4)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr23:119760629-119760629	p.D131E	3
chr23:119760717-119760717	p.S102F	2
chr23:119760065-119760065	p.*319C	1
chr23:119760844-119760844	p.R60C	1
chr23:119760388-119760388	p.G212W	1
chr23:119760593-119760593	p.A143A	1
chr23:119760099-119760099	p.V308A	1
chr23:119760860-119760860	p.K54N	1
chr23:119760396-119760396	p.E209G	1
chr23:119760607-119760607	p.W139G	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=2

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	1		3			1		1			1	2				3	6		5
# mutation	1	1		3			1		1			1	2				3	6		5
nonsynonymous SNV	1	1		3			1		1			1	1				2	4		4
synonymous SNV													1				1	2		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
chrX:119760717	p.S102F,C1GALT1C1	2
chrX:119760088	p.Y128Y,C1GALT1C1	1
chrX:119760539	p.P312T,C1GALT1C1	1
chrX:119760911	p.P311L,C1GALT1C1	1
chrX:119760090	p.F100F,C1GALT1C1	1
chrX:119760593	p.A298V,C1GALT1C1	1
chrX:119760129	p.R68Q,C1GALT1C1	1
chrX:119760607	p.Y291C,C1GALT1C1	1
chrX:119760150	p.R60C,C1GALT1C1	1
chrX:119760637	p.C270W,C1GALT1C1	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 C1GALT1C1 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 C1GALT1C1

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


AIFM1,ATG4A,ATP6AP2,C1GALT1C1,CETN2,CUL4B,CXorf56, LAMP2,LOC100303728,MCTS1,MOSPD1,MTM1,NKAP,OCRL, PSMD10,SLC25A5,TRMT2B,UBE2A,VMA21,ZBTB33,ZDHHC9	ALG5,ARF4,ATP6AP2,C1GALT1C1,CALM2,CAPZA1,CDC42, ERLEC1,ERP44,KDELR2,LAPTM4A,MAPRE1,PPCS,PSMD10, RAB1A,RAC1,SLC35B3,TFG,TM2D2,XRCC4,YWHAB

ARMCX5,ATP6AP2,BRCC3,C1GALT1C1,CUL4B,FAM104B,FUNDC2, HNRNPH2,LAMP2,MAGT1,MCTS1,MORF4L2,NKAP,NXT2, PGRMC1,PSMD10,RBMX2,SLC25A14,TSPAN6,UBE2A,VBP1	ANXA7,ARPC3,ATG3,EMC7,C1GALT1C1,CISD2,GOLT1B, LOC653566,LSM6,MAGT1,MCTS1,POMP,PPA1,PSMA1, PSMA2,PSMA4,PSMA5,SCFD1,SSR3,TMED2,TMEM165

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 C1GALT1C1

There's no related Drug.

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Cross referenced IDs for C1GALT1C1

* 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