Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	PSPH
	Gene name	phosphoserine phosphatase
	Synonyms	PSP\|PSPHD
	Cytomap	UCSC genome browser: 7p11.2
	Genomic location	chr7 :56078743-56119268
	Type of gene	protein-coding
	RefGenes	NM_004577.3,
	Ensembl id	ENSG00000146733
	Description	L-3-phosphoserine phosphataseO-phosphoserine phosphohydrolasePSPase
	Modification date	20141211
dbXrefs	MIM : 172480
	HGNC : HGNC
	Ensembl : ENSG00000146733
	HPRD : 01406
	Vega : OTTHUMG00000023441
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSPH
	BioGPS: 5723
	Gene Expression Atlas: ENSG00000146733
	The Human Protein Atlas: ENSG00000146733
Pathway	NCI Pathway Interaction Database: PSPH
	KEGG: PSPH
	REACTOME: PSPH
	ConsensusPathDB
	Pathway Commons: PSPH
Metabolism	MetaCyc: PSPH
	HUMANCyc: PSPH
Regulation	Ensembl's Regulation: ENSG00000146733
	miRBase: chr7 :56,078,743-56,119,268
	TargetScan: NM_004577
	cisRED: ENSG00000146733
Context	iHOP: PSPH
	cancer metabolism search in PubMed: PSPH
	UCL Cancer Institute: PSPH
Assigned class in ccmGDB	C

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Phenotypic Information for PSPH(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM
Orphanet
Disease	KEGG Disease: PSPH
	MedGen: PSPH (Human Medical Genetics with Condition)
	ClinVar: PSPH
Phenotype	MGI: PSPH (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PSPH related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BI053242	PSPH	1	174	7	56147536	56147710	PSPH	168	283	7	56144549	56146143
DC340871	HERC3	1	43	4	89606033	89606075	PSPH	44	540	7	56131998	56142429
BF771965	PSPH	1	72	7	56144489	56144560	TBC1D1	63	161	4	38051491	38053590
CR936749	PSPH	2	1397	7	56131983	56147817	SNRNP35	1389	1455	12	123956750	123956816
BI199927	CYB561	1	328	17	61513478	61518165	PSPH	324	759	7	56119538	56123411
BX101324	PSPH	12	89	7	56131020	56131097	ITCH	82	472	20	33096817	33097207
BF314617	CYB561	1	330	17	61513478	61518165	PSPH	326	666	7	56119538	56122197
BQ318623	MALAT1	19	101	11	65267943	65268025	PSPH	96	422	7	56122079	56124038
CB241697	PSPH	12	170	7	56125734	56126149	PSPH	164	394	7	56123443	56125764
AW606659	HYOU1	8	118	11	118922647	118923019	PSPH	112	165	7	56131325	56131378
CA430683	PSPH	18	137	7	56148239	56148358	GPATCH1	129	723	19	33600870	33605259
BU633977	PSPH	18	137	7	56148239	56148358	GPATCH1	129	666	19	33602637	33605259
AW946340	PSPH	17	109	7	56146093	56146186	PSPH	101	349	7	56142333	56146066
BC020860	SLC12A1	1	825	15	48498499	48543967	PSPH	823	1269	7	56169266	56172158
BE766917	PSPH	5	207	7	56078758	56078961	EFNB2	203	264	13	107163894	107163955
AK091504	SFXN3	1	2759	10	102797149	102800391	PSPH	2752	3218	7	56169683	56170149
BE766933	PSPH	11	216	7	56078753	56078961	EFNB2	212	273	13	107163894	107163955
CA442113	CCDC22	18	451	X	49106899	49107333	PSPH	435	523	7	56131594	56131682

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID	brca	cns	cerv	endome	haematopo	kidn	Lintest	liver	lung	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	1	10		1			1		3						1		1
GAIN (# sample)	1	10		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)

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SNV 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

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Somatic 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.

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Top 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 position	Mutation(aa)	Unique sampleID count
chr7:56085002-56085002	p.V116I	5
chr7:56087423-56087423	p.R49W	3
chr7:56088789-56088789	p.G39G	2
chr7:56088811-56088811	p.D32G	2
chr7:56088825-56088825	p.R27S	2
chr7:56079456-56079456	p.226	2
chr7:56087292-56087292	p.?	2
chr7:56079530-56079530	p.I201I	2
chr7:56087373-56087373	p.R65R	2
chr7:56079562-56079562	p.D191H	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	3		1	3	4							4	3				5	5		1
# mutation	3		1	2	2							5	3				5	5		1
nonsynonymous SNV	3		1	1	2							5	2				2	3		1
synonymous SNV				1									1				3	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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr7:56085002	p.V116I	5
chr7:56079456	p.R65R	2
chr7:56087373	p.L62V	2
chr7:56079530	p.X226X	2
chr7:56087384	p.I201I	2
chr7:56079562	p.D191H	2
chr7:56085030	p.R73W	1
chr7:56088826	p.G54R	1
chr7:56085062	p.M52T	1
chr7:56088853	p.R49L	1

Other 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

Copy 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]

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Gene Expression for PSPH

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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 PSPH

There's no related Drug.

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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