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 CAT

Basic gene info.	Gene symbol	CAT
	Gene name	catalase
	Synonyms	-
	Cytomap	UCSC genome browser: 11p13
	Genomic location	chr11 :34460471-34493607
	Type of gene	protein-coding
	RefGenes	NM_001752.3,
	Ensembl id	ENSG00000121691
	Description	-
	Modification date	20141207
dbXrefs	MIM : 115500
	HGNC : HGNC
	Ensembl : ENSG00000121691
	HPRD : 00282
	Vega : OTTHUMG00000044353
Protein	UniProt: P04040 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CAT
	BioGPS: 847
	Gene Expression Atlas: ENSG00000121691
	The Human Protein Atlas: ENSG00000121691
Pathway	NCI Pathway Interaction Database: CAT
	KEGG: CAT
	REACTOME: CAT
	ConsensusPathDB
	Pathway Commons: CAT
Metabolism	MetaCyc: CAT
	HUMANCyc: CAT
Regulation	Ensembl's Regulation: ENSG00000121691
	miRBase: chr11 :34,460,471-34,493,607
	TargetScan: NM_001752
	cisRED: ENSG00000121691
Context	iHOP: CAT
	cancer metabolism search in PubMed: CAT
	UCL Cancer Institute: CAT
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: CAT
	Familial Cancer Database: CAT

* 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
KEGG_TRYPTOPHAN_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM

Others
OMIM	115500; gene. 614097; phenotype.
Orphanet	926; Acatalasemia.
Disease	KEGG Disease: CAT
	MedGen: CAT (Human Medical Genetics with Condition)
	ClinVar: CAT
Phenotype	MGI: CAT (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CAT

Mutations for CAT

* 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
breast	CAT	chr11	34491112	34491112		chr11	34701998	34701998
breast	CAT	chr11	34491192	34491592		chr11	34535520	34535920
breast	CAT	chr11	34491528	34491528		chr11	34734557	34734557
ovary	CAT	chr11	34462335	34462355		chr11	34555336	34555356
ovary	CAT	chr11	34490992	34491012		chr11	34571498	34571518

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 CAT 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
BI024383	CAT	1	94	11	34480167	34480259	MARK3	90	185	14	103958203	103958298
BI028162	CAT	30	130	11	34480167	34480266	MARK3	126	221	14	103958203	103958298
BI028161	CAT	32	130	11	34480167	34480266	MARK3	126	222	14	103958203	103958298
BI022068	MARK3	6	104	14	103958203	103958302	CAT	100	193	11	34480167	34480259
BI024396	CAT	1	92	11	34480167	34480259	MARK3	88	183	14	103958203	103958298

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=28)	Stat. for Synonymous SNVs (# total SNVs=13)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr11:34482828-34482828	p.R363S	3
chr11:34478364-34478364	p.Q352H	2
chr11:34460565-34460565	p.A2D	2
chr11:34482829-34482829	p.R363H	1
chr11:34472585-34472585	p.A97T	1
chr11:34489936-34489936	p.K476N	1
chr11:34477579-34477579	p.L245F	1
chr11:34478296-34478296	p.E330K	1
chr11:34470811-34470811	p.R47G	1
chr11:34482847-34482847	p.N369S	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	3	1	2	10			2		2			4	1	2			5	3		6
# mutation	3	1	2	8			2		2			4	1	2			5	3		6
nonsynonymous SNV	3	1	1	5			2		1			3	1	1			5	3		4
synonymous SNV			1	3					1			1		1						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
chr11:34482828	p.R363S	3
chr11:34473654	p.R127Q	2
chr11:34473726	p.I463T	1
chr11:34478296	p.P49H	1
chr11:34489896	p.Y274Y	1
chr11:34470818	p.Q288R	1
chr11:34474692	p.G465G	1
chr11:34478311	p.Q53Q	1
chr11:34489903	p.P296S	1
chr11:34470831	p.A478V	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 CAT 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 CAT

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


APIP,CAT,CYP7A1,DENND2C,GPR85,MROH2B,HIPK1, HIPK3,KCNK10,MUC7,NRAS,PDHX,PLA2R1,POU3F4, PROK2,RNF125,RSBN1,SHISA3,TRAF6,TRIM33,TRIM44	ACO1,AOC3,CLMP,MTURN,CAT,DMGDH,DOCK11, EBF1,FERMT2,GNAI1,HRASLS5,KCNIP2,PDE8A,PEX19, PLIN1,RHOBTB3,SIK2,SORBS1,SORT1,TYRO3,VKORC1L1

ADD3,C10orf99,TCAIM,CAPRIN1,CAT,CRBN,EPB41L4B, FBXO3,FPGT,GLB1,HADH,NAALADL2,PEX11A,PEX19, PPARG,SAMM50,SNX4,SUCLG2,TMED5,TMEM135,TRUB1	ACADM,AUH,SAYSD1,CAT,CD46,CRYL1,ELAC1, FAM96A,GLOD4,GPR160,HADH,HSD17B8,HSDL2,NDUFB5, NUDT16P1,ECI2,PHYH,RMND1,SDHD,SDR42E1,SLC35A5

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 CAT

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA26099; -.
Organism-specific databases	CTD	847; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01213	catalase	approved	Fomepizole
DB03014	catalase	experimental	Heme
DB02235	catalase	experimental	Methionine Sulfoxide
DB01942	catalase	experimental	Formic Acid
DB03790	catalase	experimental	S-Dioxymethionine
DB00997	catalase	approved; investigational	Doxorubicin

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Cross referenced IDs for CAT

* 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