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 PSAP
Basic gene info.Gene symbolPSAP
Gene nameprosaposin
SynonymsGLBA|SAP1
CytomapUCSC genome browser: 10q21-q22
Genomic locationchr10 :73576054-73611082
Type of geneprotein-coding
RefGenesNM_001042465.1,
NM_001042466.1,NM_002778.2,
Ensembl idENSG00000197746
Descriptionproactivator polypeptidesphingolipid activator protein-1
Modification date20141207
dbXrefs MIM : 176801
HGNC : HGNC
Ensembl : ENSG00000197746
HPRD : 01460
Vega : OTTHUMG00000018429
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSAP
BioGPS: 5660
Gene Expression Atlas: ENSG00000197746
The Human Protein Atlas: ENSG00000197746
PathwayNCI Pathway Interaction Database: PSAP
KEGG: PSAP
REACTOME: PSAP
ConsensusPathDB
Pathway Commons: PSAP
MetabolismMetaCyc: PSAP
HUMANCyc: PSAP
RegulationEnsembl's Regulation: ENSG00000197746
miRBase: chr10 :73,576,054-73,611,082
TargetScan: NM_001042465
cisRED: ENSG00000197746
ContextiHOP: PSAP
cancer metabolism search in PubMed: PSAP
UCL Cancer Institute: PSAP
Assigned class in ccmGDBC

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

Mutations for PSAP
* 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
ovaryPSAPchr107357923973579259chr2219272992219273012
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 PSAP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW176753PSAP4785107357704773577085CKB8517514103986228103986318
BG236863PSAP564107357630373576362PSAP60205107357636573576510
AW608479PSAP1206107358781473588741ACP5196544191168757211688133
BG993981PSAP1147107357634973576496CAPG14020728562190085621967
CA433301DMTN1819982193985521940036PSAP198423107357618073576405
BF918002PSAP1454107357687473578467VRK3446567195050637350506494
CD370612PSAP16183107357605573576222HLA-DPA1180539645173384518037
BF853810RNF21311303177835566578355957PSAP297563107357932573580021
BU190440PSMA42311157884121278841523PSAP304820107357837373579633
BQ028419DMTN1820082193985521940036PSAP199424107357618073576405
BP430892DNAH6118028500465885005194PSAP181423107357635973576601
CA308179TIAL11531310121334924121335222PSAP311667107357955373585616
BE176600PSAP4127107358783873588681PSAP120534107357956973587811
BE930210PSAP34142107357999773588678PSAP140458107357698573578443
BF733880PSAP10159107357694073577090PSAP156330107357674173576914
BE707091GNAI22020635029582150296003PSAP205296107357962473580054
AW608472ACP51347191168757211688133PSAP337592107358781473588789
BG995962PSAP10213107357629973576504THBS32095341155167619155167941
BE698722PSAP2499107357926173579337PSAP89442107357710073579252
BG996012PSAP1280107357621773576496RNF1872675551228681907228682196
AA019217PSAP8145107357605773576194ABCA413039219449284194493103
BI015407PSAP16170107358005273581743IDH3B1662432026407242640801
AA632698PSAP7301107357637173576666PSAP300423107357624973576373
CA311128PSAP1982107357630373576366MAP3K5722766136878752136878956
BP391559ALDH9A1163041165636545165638556PSAP305500107357630773576501

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample 1               
GAIN (# sample)                 
LOSS (# sample) 1               
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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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=33)		Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=2)		Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr10:73579313-73579313p.D420V3
chr10:73577214-73577214p.R520H2
chr10:73594149-73594149p.V52I2
chr10:73579601-73579601p.S354S2
chr10:73581662-73581662p.P294S2
chr10:73587914-73587914p.D193H2
chr10:73579602-73579602p.S354L2
chr10:73581689-73581689p.A285T1
chr10:73579284-73579284p.Q430K1
chr10:73588696-73588696p.M172V1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 9  2 1  7 2  46 2
# mutation21 11  2 1  7 2  46 2
nonsynonymous SNV1  8  2 1  5 2  15 1
synonymous SNV11 3       2    31 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
chr10:73581662p.P296T,PSAP2
chr10:73587834p.S486L,PSAP1
chr10:73578385p.A287T,PSAP1
chr10:73591639p.D64N,PSAP1
chr10:73579613p.G482R,PSAP1
chr10:73587852p.M281I,PSAP1
chr10:73578462p.P62T,PSAP1
chr10:73591662p.L435M,PSAP1
chr10:73579616p.F272L,PSAP1
chr10:73587857p.L49L,PSAP1

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 PSAP 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 PSAP

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

ADAP2,C3AR1,CD33,CD4,CD68,CTSB,EMILIN2,
HAVCR2,ITGB2,LAIR1,LAPTM5,LGMN,LRRC25,MS4A6A,
NCKAP1L,PLEKHO2,PSAP,SIGLEC7,SIGLEC9,SLC7A7,SLCO2B1		ALDH3B1,CD4,CD68,CTSA,CTSB,FTL,COLGALT1,
HAVCR2,LILRB4,LOXL3,LRRC25,MGAT1,NCF2,NFAM1,
PI4K2A,PLA2G15,PSAP,RENBP,SLC15A3,SPI1,TRPV2

AIF1,C1QC,CD300C,CD4,CD84,CD86,CMKLR1,
FPR3,GPNMB,HAVCR2,ITGB2,LAIR1,LAPTM5,LILRB4,
LRRC25,PLD3,PLEKHO2,PSAP,SIGLEC7,SPI1,TYROBP		ACAA2,SOWAHD,AOAH,BCAS4,WBP1L,CCNDBP1,COG8,
DDX19B,ATG13,MAN2B1,MB,DNMBP-AS1,PSAP,PTCRA,
RNF135,SAT1,SARAF,TRAF7,TTC22,ZBTB3,ZSWIM3
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 PSAP


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