Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolCAT
Gene namecatalase
Synonyms-
CytomapUCSC genome browser: 11p13
Genomic locationchr11 :34460471-34493607
Type of geneprotein-coding
RefGenesNM_001752.3,
Ensembl idENSG00000121691
Description-
Modification date20141207
dbXrefs MIM : 115500
HGNC : HGNC
Ensembl : ENSG00000121691
HPRD : 00282
Vega : OTTHUMG00000044353
ProteinUniProt: P04040
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CAT
BioGPS: 847
Gene Expression Atlas: ENSG00000121691
The Human Protein Atlas: ENSG00000121691
PathwayNCI Pathway Interaction Database: CAT
KEGG: CAT
REACTOME: CAT
ConsensusPathDB
Pathway Commons: CAT
MetabolismMetaCyc: CAT
HUMANCyc: CAT
RegulationEnsembl's Regulation: ENSG00000121691
miRBase: chr11 :34,460,471-34,493,607
TargetScan: NM_001752
cisRED: ENSG00000121691
ContextiHOP: CAT
cancer metabolism search in PubMed: CAT
UCL Cancer Institute: CAT
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for CAT(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_TRYPTOPHAN_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM

check002.gifOthers
OMIM 115500; gene.
614097; phenotype.
Orphanet 926; Acatalasemia.
DiseaseKEGG Disease: CAT
MedGen: CAT (Human Medical Genetics with Condition)
ClinVar: CAT
PhenotypeMGI: CAT (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastCATchr113449111234491112chr113470199834701998
breastCATchr113449119234491592chr113453552034535920
breastCATchr113449152834491528chr113473455734734557
ovaryCATchr113446233534462355chr113455533634555356
ovaryCATchr113449099234491012chr113457149834571518
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CAT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI024383CAT194113448016734480259MARK39018514103958203103958298
BI028162CAT30130113448016734480266MARK312622114103958203103958298
BI028161CAT32130113448016734480266MARK312622214103958203103958298
BI022068MARK3610414103958203103958302CAT100193113448016734480259
BI024396CAT192113448016734480259MARK38818314103958203103958298

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2       1     1  
GAIN (# sample)2       1     1  
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr11:34482828-34482828p.R363S3
chr11:34478364-34478364p.Q352H2
chr11:34460565-34460565p.A2D2
chr11:34472585-34472585p.A97T1
chr11:34482829-34482829p.R363H1
chr11:34477579-34477579p.L245F1
chr11:34489936-34489936p.K476N1
chr11:34470811-34470811p.R47G1
chr11:34478296-34478296p.E330K1
chr11:34472631-34472631p.R112Q1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample31210  2 2  412  53 6
# mutation3128  2 2  412  53 6
nonsynonymous SNV3115  2 1  311  53 4
synonymous SNV  13    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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr11:34482828p.R363S3
chr11:34473654p.R127Q2
chr11:34473726p.P49H1
chr11:34478296p.Y274Y1
chr11:34470818p.I463T1
chr11:34489896p.Q53Q1
chr11:34474692p.Q288R1
chr11:34478311p.G465G1
chr11:34470831p.H63H1
chr11:34489903p.P296S1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA26099; -.
Organism-specific databasesCTD 847; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01213catalaseapprovedFomepizole
DB03014catalaseexperimentalHeme
DB02235catalaseexperimentalMethionine Sulfoxide
DB01942catalaseexperimentalFormic Acid
DB03790catalaseexperimentalS-Dioxymethionine
DB00997catalaseapproved; investigationalDoxorubicin


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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



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