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 ACP2
Basic gene info.Gene symbolACP2
Gene nameacid phosphatase 2, lysosomal
SynonymsLAP
CytomapUCSC genome browser: 11p11.2|11p12-p11
Genomic locationchr11 :47260852-47270457
Type of geneprotein-coding
RefGenesNM_001302489.1,
NM_001302490.1,NM_001302491.1,NM_001302492.1,NM_001610.3,
NM_001131064.1,
Ensembl idENSG00000134575
Descriptionlysosomal acid phosphatase
Modification date20141207
dbXrefs MIM : 171650
HGNC : HGNC
Ensembl : ENSG00000134575
HPRD : 01375
Vega : OTTHUMG00000166949
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACP2
BioGPS: 53
Gene Expression Atlas: ENSG00000134575
The Human Protein Atlas: ENSG00000134575
PathwayNCI Pathway Interaction Database: ACP2
KEGG: ACP2
REACTOME: ACP2
ConsensusPathDB
Pathway Commons: ACP2
MetabolismMetaCyc: ACP2
HUMANCyc: ACP2
RegulationEnsembl's Regulation: ENSG00000134575
miRBase: chr11 :47,260,852-47,270,457
TargetScan: NM_001302489
cisRED: ENSG00000134575
ContextiHOP: ACP2
cancer metabolism search in PubMed: ACP2
UCL Cancer Institute: ACP2
Assigned class in ccmGDBC

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Phenotypic Information for ACP2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACP2
Familial Cancer Database: ACP2
* 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_RIBOFLAVIN_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ACP2
MedGen: ACP2 (Human Medical Genetics with Condition)
ClinVar: ACP2
PhenotypeMGI: ACP2 (International Mouse Phenotyping Consortium)
PhenomicDB: ACP2

Mutations for ACP2
* 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
pancreasACP2chr114726337547263395DDB2chr114724225747242277
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 ACP2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA582448ACP296438114726735347270356MRVI1-AS1428540111059005310590165
AK097626ACP211919114726843847270356KIRREL31912206711126792984126793353

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

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=31)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr11:47269678-47269678p.R41C2
chr11:47266897-47266897p.L200L2
chr11:47261788-47261788p.A384V2
chr11:47267093-47267093p.R161C2
chr11:47269233-47269233p.R86C2
chr11:47264443-47264443p.F323F2
chr11:47267247-47267247p.I146V1
chr11:47269242-47269242p.L83V1
chr11:47264624-47264624p.E303K1
chr11:47266884-47266884p.W204L1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  8  1 1  211  44 3
# mutation1  8  1 1  211  44 3
nonsynonymous SNV   7  1 1  211  12 2
synonymous SNV1  1            32 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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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
chr11:47264838p.G194V1
chr11:47267305p.R181Q1
chr11:47264856p.R414H1
chr11:47267352p.S180F1
chr11:47261698p.R161C1
chr11:47266884p.V402I1
chr11:47267355p.I146V,ACP21
chr11:47261735p.Q352Q1
chr11:47266885p.P132P,ACP21
chr11:47269227p.R330R1

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 ACP2 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 ACP2

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

ACP2,ARFGAP2,C1QA,DDB2,FUCA1,GRN,IFI30,
LMAN2,MPDU1,NDUFS3,NR1H3,PACSIN3,PEX16,PSMB10,
PSMC3,PSME1,PSME2,SIL1,TYMP,TYROBP,VAMP8
ABHD12,ACP2,ALDH3B1,AP2S1,ARPC1B,ATOX1,C1orf85,
CSTB,CTSD,CTSZ,FCGRT,GRN,HPCAL1,NAGPA,
PLD3,PSAP,LAMTOR2,SIL1,SLC8B1,SMPD1,TYROBP

ABI3,ACP2,AIF1,C10orf54,C1QA,C1QB,C1QC,
CTSD,FCGR1B,GNAI2,IFI30,IL4I1,ITGB2,LAIR1,
MGAT1,OSCAR,PLD3,SLAMF8,SLC15A3,SPI1,TYROBP
ACP2,CTSZ,ESPN,FAM83F,HECTD3,ITGA3,LASP1,
MAPK3,PARP12,PLEKHG6,PRKCD,PRKCZ,PRSS8,SESN2,
SLC9A3R1,SPINT1,SRC,TNIP1,TOM1,TRIM14,VPS33B
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 ACP2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01033acid phosphatase 2, lysosomalapprovedMercaptopurine
DB00563acid phosphatase 2, lysosomalapprovedMethotrexate


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Cross referenced IDs for ACP2
* 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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