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 ACP1
Basic gene info.Gene symbolACP1
Gene nameacid phosphatase 1, soluble
SynonymsHAAP
CytomapUCSC genome browser: 2p25
Genomic locationchr2 :264868-278282
Type of geneprotein-coding
RefGenesNM_001040649.2,
NM_004300.3,NM_007099.3,NR_024080.1,NM_177554.1,
Ensembl idENSG00000143727
DescriptionLMW-PTPLMW-PTPaseacid phosphatase of erythrocyteadipocyte acid phosphatasecytoplasmic phosphotyrosyl protein phosphataselow molecular weight cytosolic acid phosphataselow molecular weight phosphotyrosine protein phosphataseprotein tyrosine phosphat
Modification date20141207
dbXrefs MIM : 171500
HGNC : HGNC
Ensembl : ENSG00000143727
HPRD : 08881
Vega : OTTHUMG00000086933
ProteinUniProt: P24666
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACP1
BioGPS: 52
Gene Expression Atlas: ENSG00000143727
The Human Protein Atlas: ENSG00000143727
PathwayNCI Pathway Interaction Database: ACP1
KEGG: ACP1
REACTOME: ACP1
ConsensusPathDB
Pathway Commons: ACP1
MetabolismMetaCyc: ACP1
HUMANCyc: ACP1
RegulationEnsembl's Regulation: ENSG00000143727
miRBase: chr2 :264,868-278,282
TargetScan: NM_001040649
cisRED: ENSG00000143727
ContextiHOP: ACP1
cancer metabolism search in PubMed: ACP1
UCL Cancer Institute: ACP1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ACP1 in cancer cell metabolism1. Pedersen K, Canals F, Prat A, Tabernero J, Arribas J (2014) PELO negatively regulates HER receptor signalling and metastasis. Oncogene 33: 1190-1197. doi: 10.1038/onc.2013.35. go to article
2. Wright WC, Daniels WP, Fogh J (1981) Distinction of seventy-one cultured human tumor cell lines by polymorphic enzyme analysis. J Natl Cancer Inst 66: 239-247. go to article

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Phenotypic Information for ACP1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACP1
Familial Cancer Database: ACP1
* 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 171500; gene.
171500; gene.
Orphanet
DiseaseKEGG Disease: ACP1
MedGen: ACP1 (Human Medical Genetics with Condition)
ClinVar: ACP1
PhenotypeMGI: ACP1 (International Mouse Phenotyping Consortium)
PhenomicDB: ACP1

Mutations for ACP1
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ACP1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=19)
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
chr2:272081-272081p.P56fs*92
chr2:277079-277079p.P131P2
chr2:272128-272128p.P70L2
chr2:277002-277002p.Q106*2
chr2:277291-277291p.E155V2
chr2:277034-277034p.L116L2
chr2:277050-277050p.P122S1
chr2:271865-271865p.?1
chr2:272077-272077p.G53V1
chr2:277057-277057p.K124T1

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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  1  1 1  321  31 5
# mutation1  3  1 1  431  31 5
nonsynonymous SNV   2  1 1  131  2  5
synonymous SNV1  1       3    11  
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
chr2:277250p.T141T,ACP12
chr2:272236p.G106V2
chr2:271881p.D136D,ACP11
chr2:277020p.S20L,ACP11
chr2:271918p.T32T,ACP11
chr2:277042p.E155E,ACP11
chr2:272047p.D43G,ACP11
chr2:277050p.T95A,ACP11
chr2:272202p.A96V1
chr2:277076p.T103M1

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 ACP1 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 ACP1

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

ACP1,BOLA3,COX7A2L,CPSF3,DPY30,E2F6,FAM136A,
IAH1,MDH1,MEMO1,NOL10,PNO1,RNASEH1,RPS7,
SF3B14,SH3YL1,SNRPG,TMEM18,TSSC1,USP39,YWHAQ
ACP1,ATXN10,CCNB1IP1,DENR,DUS4L,EIF3E,ENOPH1,
FAM103A1,FARSB,GTF2F2,NIFK,MRPL3,MRPS35,OLA1,
PPA2,RPL15,RSL24D1,TMEM5,TMEM69,TOMM20,TTC19

ACP1,CCT4,CCT7,CPSF3,DPY30,FAM136A,GPN1,
MEMO1,METTL5,NIFK,MRPL30,OLA1,PNO1,PTCD3,
RPS7,SF3B14,SNRPG,SUMO1,TPRKB,USP39,YWHAQ
ACP1,ALG5,ATG3,CCNC,CNIH1,EBAG9,EEF1B2,
FAM96A,MAGT1,MRPL48,MRPS22,PDCD2,POC1B,PPA2,
PSMD10,RCHY1,SEP15,SRP9,TGDS,TXNDC12,UQCRH
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 ACP1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P24666; -.
ChemistryChEMBL CHEMBL4903; -.
ChemistryBindingDB P24666; -.
ChemistryChEMBL CHEMBL4903; -.
Organism-specific databasesPharmGKB PA24446; -.
Organism-specific databasesPharmGKB PA24446; -.
Organism-specific databasesCTD 52; -.
Organism-specific databasesCTD 52; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00173acid phosphatase 1, solubleapproved; nutraceuticalAdenine
DB04214acid phosphatase 1, solubleexperimental4-Nitrophenyl Phosphate


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Cross referenced IDs for ACP1
* 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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