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 PSAT1
Basic gene info.Gene symbolPSAT1
Gene namephosphoserine aminotransferase 1
SynonymsEPIP|NLS2|PSA|PSAT|PSATD
CytomapUCSC genome browser: 9q21.2
Genomic locationchr9 :80912058-80945009
Type of geneprotein-coding
RefGenesNM_021154.4,
NM_058179.3,
Ensembl idENSG00000135069
Descriptionendometrial progesterone-induced proteinphosphohydroxythreonine aminotransferasephosphoserine aminotransferase
Modification date20141207
dbXrefs MIM : 610936
HGNC : HGNC
Ensembl : ENSG00000135069
HPRD : 17918
Vega : OTTHUMG00000020066
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSAT1
BioGPS: 29968
Gene Expression Atlas: ENSG00000135069
The Human Protein Atlas: ENSG00000135069
PathwayNCI Pathway Interaction Database: PSAT1
KEGG: PSAT1
REACTOME: PSAT1
ConsensusPathDB
Pathway Commons: PSAT1
MetabolismMetaCyc: PSAT1
HUMANCyc: PSAT1
RegulationEnsembl's Regulation: ENSG00000135069
miRBase: chr9 :80,912,058-80,945,009
TargetScan: NM_021154
cisRED: ENSG00000135069
ContextiHOP: PSAT1
cancer metabolism search in PubMed: PSAT1
UCL Cancer Institute: PSAT1
Assigned class in ccmGDBC

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Phenotypic Information for PSAT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSAT1
Familial Cancer Database: PSAT1
* 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: PSAT1
MedGen: PSAT1 (Human Medical Genetics with Condition)
ClinVar: PSAT1
PhenotypeMGI: PSAT1 (International Mouse Phenotyping Consortium)
PhenomicDB: PSAT1

Mutations for PSAT1
* 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
ovaryPSAT1chr98093454380934563chr98088344880883468
ovaryPSAT1chr98093730980937329chr98084140980841429
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 PSAT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF989450CPNE433103131966378131966685PSAT130540098094422680944321
AA328351ANKIB111014979188709791887137PSAT114231798093847580938650
BC001618PSAT11217898091207480945011SLC1A42165371626524944865250999

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=24)
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
chr9:80916919-80916919p.E57D2
chr9:80919698-80919698p.C80Y2
chr9:80919712-80919712p.A85P2
chr9:80921287-80921287p.C152Y1
chr9:80923420-80923420p.L221F1
chr9:80943085-80943085p.L330L1
chr9:80919745-80919745p.G96R1
chr9:80921319-80921319p.D163N1
chr9:80916926-80916926p.V60L1
chr9:80923424-80923424p.R222Q1

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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
# sample   51   1  52   7318
# mutation   52   1  72   7419
nonsynonymous SNV   52   1  42   2315
synonymous SNV           3    51 4
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
chr9:80916919p.C80Y,PSAT12
chr9:80919698p.E57D,PSAT12
chr9:80919828p.V60L,PSAT11
chr9:80921375p.D167N,PSAT11
chr9:80943085p.V292V,PSAT11
chr9:80919840p.R61W,PSAT11
chr9:80923337p.A171T,PSAT11
chr9:80916926p.K317N,PSAT11
chr9:80943903p.R61R,PSAT11
chr9:80921233p.V172V,PSAT11

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 PSAT1 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 PSAT1

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

ASNS,B3GNT5,BCL11A,AUNIP,MSANTD3,C9orf40,CDC20,
CDCA7,CDCA8,CEBPG,CENPA,FAM136A,FOXM1,IFRD1,
KCMF1,KIF2C,L3MBTL4,NDC80,ORC1,PSAT1,TEX10
ABCC6,ADIPOR2,AK3___AK4,ALDH9A1,ALG9,CYP2C18,DGAT2,
FMOD,GPAM,FFAR4,LAIR1,TENM4,PLA2G4A,PPP2R1B,
PRRT4,PSAT1,PTPLB,SEMA4F,SPRY4,SSC4D,VPS45

ASNS,ATF4,CEP78,CHAC1,FXN,GARS,GRPEL2,
H2AFZ,IARS,MARS,MTHFD2,NEIL3,PHGDH,PSAT1,
SLC4A5,SLC7A5,STC2,TARS,TUBE1,XPOT,YARS
C2,C2CD4A,CDC25B,CHI3L1,CLDN14,EMILIN2,FCGR3A,
FCN1,FCN3,HK3,LILRA3,LILRA6,LILRB2,MTHFD1L,
PSAT1,RNASE2,SPINK4,TCN1,TLR2,TNIP3,ZAR1L
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 PSAT1
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
DB00114phosphoserine aminotransferase 1nutraceuticalPyridoxal Phosphate
DB00142phosphoserine aminotransferase 1approved; nutraceuticalL-Glutamic Acid
DB02327phosphoserine aminotransferase 1experimental2-[2-(2-Hydroxy-Ethoxy)-Ethoxy]-Ethanol


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Cross referenced IDs for PSAT1
* 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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