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 PSPH
Basic gene info.Gene symbolPSPH
Gene namephosphoserine phosphatase
SynonymsPSP|PSPHD
CytomapUCSC genome browser: 7p11.2
Genomic locationchr7 :56078743-56119268
Type of geneprotein-coding
RefGenesNM_004577.3,
Ensembl idENSG00000146733
DescriptionL-3-phosphoserine phosphataseO-phosphoserine phosphohydrolasePSPase
Modification date20141211
dbXrefs MIM : 172480
HGNC : HGNC
Ensembl : ENSG00000146733
HPRD : 01406
Vega : OTTHUMG00000023441
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSPH
BioGPS: 5723
Gene Expression Atlas: ENSG00000146733
The Human Protein Atlas: ENSG00000146733
PathwayNCI Pathway Interaction Database: PSPH
KEGG: PSPH
REACTOME: PSPH
ConsensusPathDB
Pathway Commons: PSPH
MetabolismMetaCyc: PSPH
HUMANCyc: PSPH
RegulationEnsembl's Regulation: ENSG00000146733
miRBase: chr7 :56,078,743-56,119,268
TargetScan: NM_004577
cisRED: ENSG00000146733
ContextiHOP: PSPH
cancer metabolism search in PubMed: PSPH
UCL Cancer Institute: PSPH
Assigned class in ccmGDBC

Top
Phenotypic Information for PSPH(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSPH
Familial Cancer Database: PSPH
* 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_GLYCINE_SERINE_AND_THREONINE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for PSPH
* 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 PSPH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI053242PSPH117475614753656147710PSPH16828375614454956146143
DC340871HERC314348960603389606075PSPH4454075613199856142429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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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample110 1  1 3     1 1
GAIN (# sample)110 1  1 3     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)

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=5

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=20)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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
chr7:56085002-56085002p.V116I5
chr7:56087423-56087423p.R49W3
chr7:56088789-56088789p.G39G2
chr7:56088811-56088811p.D32G2
chr7:56088825-56088825p.R27S2
chr7:56079456-56079456p.*226*2
chr7:56087292-56087292p.?2
chr7:56079530-56079530p.I201I2
chr7:56087373-56087373p.R65R2
chr7:56079562-56079562p.D191H2

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample3 134      43   55 1
# mutation3 122      53   55 1
nonsynonymous SNV3 112      52   23 1
synonymous SNV   1        1   32  
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
chr7:56085002p.V116I5
chr7:56079456p.I201I2
chr7:56087373p.D191H2
chr7:56079530p.R65R2
chr7:56087384p.L62V2
chr7:56079562p.X226X2
chr7:56088813p.L219M1
chr7:56085030p.E46Q1
chr7:56088826p.I31I1
chr7:56085062p.R27T1

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 PSPH 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 PSPH

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

C2orf80,CCT6A,CHCHD2,CNGB1,DEFB118,DKFZp434L192,EGFR,
ELAVL4,GBAS,COLGALT2,LANCL2,MRPS17,NPPB,PHKG1,
PSPH,SEC61G,SERPINB13,SLC6A2,SUMF2,VOPP1,ZNF713
ACAA1,ACY1,ALG1,ATP6V0E2,ELP6,CBY1,CDK5,
DNASE2,HIST1H4J,ILVBL,LHPP,P4HB,PHB,PSPH,
PTPMT1,RAC3,RER1,SMUG1,SUMF2,TSTD1,VPS16

AHCY,ASNS,BZW2,OSER1,C20orf24,MALSU1,COA1,
CCT6A,CHCHD2,COMMD7,COPS6,EIF2S2,NUPL2,ORC5,
PDRG1,PNO1,PSMA2,PSMA7,PSPH,RPS21,STARD3NL
ADSL,AHCY,APEX1,BCS1L,RHNO1,CIAO1,DANCR,
LGTN,MRPL45,MRPS26,MRPS27,PCBD1,PDCD2L,PEMT,
POMGNT1,PSPH,RPS5,RPUSD4,SMYD2,ZCCHC4,ZNF511
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 PSPH


There's no related Drug.
Top
Cross referenced IDs for PSPH
* 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