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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for PYCR1
check button Gene summary
Basic gene informationGene symbolPYCR1
Gene namepyrroline-5-carboxylate reductase 1
SynonymsARCL2B|ARCL3B|P5C|P5CR|PIG45|PP222|PRO3|PYCR
CytomapUCSC genome browser: 17q25.3
Type of geneprotein-coding
RefGenesNM_001282279.1,
NM_001282280.1,NM_001282281.1,NM_006907.3,NM_153824.2,
DescriptionP5C reductase 1proliferation-inducing protein 45pyrroline-5-carboxylate reductase 1, mitochondrial
Modification date20141207
dbXrefs MIM : 179035
HGNC : HGNC
Ensembl : ENSG00000183010
HPRD : 01528
Vega : OTTHUMG00000178436
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PYCR1
BioGPS: 5831
PathwayNCI Pathway Interaction Database: PYCR1
KEGG: PYCR1
REACTOME: PYCR1
Pathway Commons: PYCR1
ContextiHOP: PYCR1
ligand binding site mutation search in PubMed: PYCR1
UCL Cancer Institute: PYCR1
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)PancreasStomach
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)PAADSTAD
Reference showing the relevant tissue of PYCR1
Description by TissGene annotationsRisk TissGene in RFS
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0006561proline biosynthetic process16730026
GO:0006561proline biosynthetic process16730026


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TissGeneExp for PYCR1

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
BLCA0.206470519-2.4306084282.6370789476.75E-097.51E-07
BRCA0.963752975-1.3373900072.3011429821.94E-374.51E-36
KICH-2.024953481-3.9432734811.918321.38E-054.25E-05
LUAD1.352480864-2.2723725853.6248534481.74E-493.90E-46
PRAD2.2148378270.6268416731.5879961545.23E-192.93E-16
KIRC-2.899233648-3.9951517031.0959180561.03E-062.63E-06
KIRP-1.267979481-3.9804857312.712506252.74E-092.33E-08
COAD1.532920519-0.033810251.5667307697.25E-131.99E-11
LUSC0.725484244-2.0744196772.7999039222.77E-291.06E-27
STAD0.912495519-0.8778888561.7903843750.0001850.001312508


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TissGene-miRNA for PYCR1

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for PYCR1
TissGeneSNV for PYCR1

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.G236RHNSC1
p.D165VPRAD1
p.R119CBLCA1
p.R266WUCEC1
p.G297ESARC1
p.H240YSKCM1
p.S233FBLCA1
p.G297RLUSC1
p.G248VPRAD1
p.K17NKIRC1
p.T160MPRAD1
p.V24ISARC1
p.T171MSKCM1
p.F250LLIHC1
p.F13VSTAD1
p.L148PSKCM1
p.V99IUCEC1
p.T171MLUAD1
p.C159FPAAD1
p.V99AUCEC1


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TissGeneCNV for PYCR1

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for PYCR1

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
TCGAfusionPortalPRADABRCATCGA-AN-A0FX-01APYCR1-NOTUMOut-of-frameChr17:79893213Chr17:79916871


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TissGeneNet for PYCR1

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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COAD (tumor)COAD (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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HNSC (tumor)HNSC (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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KICH (tumor)KICH (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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KIRC (tumor)KIRC (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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KIRP (tumor)KIRP (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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LIHC (tumor)LIHC (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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LUAD (tumor)LUAD (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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LUSC (tumor)LUSC (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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PRAD (tumor)PRAD (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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STAD (tumor)STAD (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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THCA (tumor)THCA (normal)
PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (tumor)PYCR1, SUMO2, CUL3, NUDT21, CDK2AP2, BNIPL (normal)
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TissGeneProg for PYCR1

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for PYCR1
TissGeneDrug for PYCR1

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status
DB00172L-ProlineSmall moleculeApproved|Nutraceutical


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TissGeneDisease for PYCR1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C2751987Cutis Laxa, Autosomal Recessive, Type IIB5BeFree,CLINVAR,CTD_human,ORPHANET,UNIPROT
umls:C0010495Cutis Laxa3BeFree,CTD_human
umls:C0268351Cutis Laxa, Autosomal Recessive, Type I3BeFree
umls:C0025362Mental Retardation2BeFree
umls:C3280799CUTIS LAXA, AUTOSOMAL RECESSIVE, TYPE IIIB2CLINVAR,ORPHANET,UNIPROT
umls:C0023470Myeloid Leukemia1BeFree
umls:C0025007Measles1BeFree
umls:C0033300Progeria1CTD_human
umls:C0175754Agenesis of corpus callosum1BeFree
umls:C0376358Malignant neoplasm of prostate1BeFree
umls:C0431369Dysgenesis of corpus callosum1BeFree
umls:C0600139Prostate carcinoma1BeFree
umls:C0872410Posturing1BeFree
umls:C1704272Benign Prostatic Hyperplasia1BeFree
umls:C0432255Geroderma osteodysplastica0ORPHANET