Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 CTSA
Basic gene info.Gene symbolCTSA
Gene namecathepsin A
SynonymsGLB2|GSL|NGBE|PPCA|PPGB
CytomapUCSC genome browser: 20q13.1
Genomic locationchr20 :44519590-44527458
Type of geneprotein-coding
RefGenesNM_000308.2,
NM_001127695.1,NM_001167594.1,
Ensembl idENSG00000064601
Descriptionbeta-galactosidase 2beta-galactosidase protective proteincarboxypeptidase Ccarboxypeptidase Lcarboxypeptidase Y-like kininasecarboxypeptidase-Ldeamidaselysosomal carboxypeptidase Alysosomal protective proteinprotective protein cathepsin Aurinary
Modification date20141207
dbXrefs MIM : 613111
HGNC : HGNC
Ensembl : ENSG00000064601
HPRD : 02020
Vega : OTTHUMG00000033078
ProteinUniProt: P10619
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CTSA
BioGPS: 5476
Gene Expression Atlas: ENSG00000064601
The Human Protein Atlas: ENSG00000064601
PathwayNCI Pathway Interaction Database: CTSA
KEGG: CTSA
REACTOME: CTSA
ConsensusPathDB
Pathway Commons: CTSA
MetabolismMetaCyc: CTSA
HUMANCyc: CTSA
RegulationEnsembl's Regulation: ENSG00000064601
miRBase: chr20 :44,519,590-44,527,458
TargetScan: NM_000308
cisRED: ENSG00000064601
ContextiHOP: CTSA
cancer metabolism search in PubMed: CTSA
UCL Cancer Institute: CTSA
Assigned class in ccmGDBB - This gene belongs to cancer gene.

Top
Phenotypic Information for CTSA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CTSA
Familial Cancer Database: CTSA
* 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
REACTOME_GLYCOSPHINGOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 256540; phenotype.
613111; gene.
Orphanet 351; Galactosialidosis.
DiseaseKEGG Disease: CTSA
MedGen: CTSA (Human Medical Genetics with Condition)
ClinVar: CTSA
PhenotypeMGI: CTSA (International Mouse Phenotyping Consortium)
PhenomicDB: CTSA

Mutations for CTSA
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 CTSA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM842710CTSA1454204451995044521067PIGQ44955916633475633585
BM760783CTSA1453204451995044521067PIGQ44869516633475633721
AA535995GSTP13203116735392567354124CTSA192251204452264544522704
AA625344FXR174933180633869180633888CTSA87531204452093744522709
BF823719CTSA1189204452665844527103ATP6V0A41823497138406708138413610

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

Top
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=6

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=35)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=9)
Stat. for Insertions
(# total SNVs=1)

Top
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
chr20:44520238-44520240p.L29delL6
chr20:44522691-44522691p.D271Y2
chr20:44520375-44520375p.G74G2
chr20:44521861-44521861p.G219G2
chr20:44521379-44521379p.F172V2
chr20:44520659-44520659p.P118H1
chr20:44523660-44523660p.R344C1
chr20:44526445-44526445p.K436N1
chr20:44521404-44521404p.R180H1
chr20:44520237-44520238p.L29fs*1301

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 2    2  4211 54 10
# mutation11 2    2  4211 54 13
nonsynonymous SNV11      2  2211 21 11
synonymous SNV   2       2    33 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])

Top
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
chr20:44522691p.D254H,CTSA2
chr20:44521454p.A456T,CTSA1
chr20:44523469p.S218P,CTSA1
chr20:44520336p.A456A,CTSA1
chr20:44527020p.Y224H,CTSA1
chr20:44521472p.M459I,CTSA1
chr20:44523539p.K61K,CTSA1
chr20:44520573p.R232R,CTSA1
chr20:44527059p.F472L,CTSA1
chr20:44521484p.K89K,CTSA1

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 CTSA 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]

Top
Gene Expression for CTSA

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ACOT8,ADRM1,C20orf24,CD63,CHPF,CTSA,DNTTIP1,
GAA,GALNS,GRN,P4HA2,PIGT,PLA2G15,PSMA7,
SH3BGRL3,SLC16A3,SLC35C2,SNX21,TMED9,TMEM208,VAC14
TANGO2,CD248,CD63,CRYL1,CST3,CSTB,CTSA,
FCGRT,FTL,COLGALT1,GMFG,GNAI2,LGALS1,MARCH2,
MGAT1,PLXND1,PSAP,RENBP,RNASE1,TCN2,TPD52L2

ACOT8,ARFGEF2,BLCAP,SPATA25,CHMP4B,CLCN7,CTSA,
DYNLRB1,LAMP1,NEU1,OSBPL2,PIGT,PIGU,PPP1R3D,
RAB22A,RALY,SERINC3,SLC35C2,SNX21,TOMM34,ZSWIM1
STPG1,CACFD1,CDH1,CDKN2B,CLCN2,CLIP2,CNNM4,
CTSA,GBA,MARVELD3,MGLL,MYO1D,NR2F6,PEX26,
PRR15,PRSS8,RAB40C,SERINC2,SFXN1,SPINT1,TSPAN7
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for CTSA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P10619; -.
ChemistryChEMBL CHEMBL6115; -.
Organism-specific databasesPharmGKB PA33572; -.
Organism-specific databasesCTD 5476; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB03014cathepsin AexperimentalHeme
DB07690cathepsin Aexperimental(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID


Top
Cross referenced IDs for CTSA
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas