TissGeneSummary for PYCR1 |
Gene summary |
Basic gene information | Gene symbol | PYCR1 |
Gene name | pyrroline-5-carboxylate reductase 1 | |
Synonyms | ARCL2B|ARCL3B|P5C|P5CR|PIG45|PP222|PRO3|PYCR | |
Cytomap | UCSC genome browser: 17q25.3 | |
Type of gene | protein-coding | |
RefGenes | NM_001282279.1, NM_001282280.1,NM_001282281.1,NM_006907.3,NM_153824.2, | |
Description | P5C reductase 1proliferation-inducing protein 45pyrroline-5-carboxylate reductase 1, mitochondrial | |
Modification date | 20141207 | |
dbXrefs | MIM : 179035 | |
HGNC : HGNC | ||
Ensembl : ENSG00000183010 | ||
HPRD : 01528 | ||
Vega : OTTHUMG00000178436 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PYCR1 | |
BioGPS: 5831 | ||
Pathway | NCI Pathway Interaction Database: PYCR1 | |
KEGG: PYCR1 | ||
REACTOME: PYCR1 | ||
Pathway Commons: PYCR1 | ||
Context | iHOP: PYCR1 | |
ligand binding site mutation search in PubMed: PYCR1 | ||
UCL Cancer Institute: PYCR1 | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | TiGER,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 annotations | Risk 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. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID | GO:0006561 | proline biosynthetic process | 16730026 | GO:0006561 | proline biosynthetic process | 16730026 |
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TissGeneExp for PYCR1 |
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 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 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. |
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) |
- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
BLCA | 0.206470519 | -2.430608428 | 2.637078947 | 6.75E-09 | 7.51E-07 |
BRCA | 0.963752975 | -1.337390007 | 2.301142982 | 1.94E-37 | 4.51E-36 |
KICH | -2.024953481 | -3.943273481 | 1.91832 | 1.38E-05 | 4.25E-05 |
LUAD | 1.352480864 | -2.272372585 | 3.624853448 | 1.74E-49 | 3.90E-46 |
PRAD | 2.214837827 | 0.626841673 | 1.587996154 | 5.23E-19 | 2.93E-16 |
KIRC | -2.899233648 | -3.995151703 | 1.095918056 | 1.03E-06 | 2.63E-06 |
KIRP | -1.267979481 | -3.980485731 | 2.71250625 | 2.74E-09 | 2.33E-08 |
COAD | 1.532920519 | -0.03381025 | 1.566730769 | 7.25E-13 | 1.99E-11 |
LUSC | 0.725484244 | -2.074419677 | 2.799903922 | 2.77E-29 | 1.06E-27 |
STAD | 0.912495519 | -0.877888856 | 1.790384375 | 0.000185 | 0.001312508 |
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TissGene-miRNA for PYCR1 |
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 type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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TissGeneMut for PYCR1 |
TissGeneSNV for PYCR1 |
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. |
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) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.G236R | HNSC | 1 |
p.D165V | PRAD | 1 |
p.R119C | BLCA | 1 |
p.R266W | UCEC | 1 |
p.G297E | SARC | 1 |
p.H240Y | SKCM | 1 |
p.S233F | BLCA | 1 |
p.G297R | LUSC | 1 |
p.G248V | PRAD | 1 |
p.K17N | KIRC | 1 |
p.T160M | PRAD | 1 |
p.V24I | SARC | 1 |
p.T171M | SKCM | 1 |
p.F250L | LIHC | 1 |
p.F13V | STAD | 1 |
p.L148P | SKCM | 1 |
p.V99I | UCEC | 1 |
p.T171M | LUAD | 1 |
p.C159F | PAAD | 1 |
p.V99A | UCEC | 1 |
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TissGeneCNV for PYCR1 |
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) |
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TissGeneFusions for PYCR1 |
Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
TCGAfusionPortal | PRADA | BRCA | TCGA-AN-A0FX-01A | PYCR1-NOTUM | Out-of-frame | Chr17:79893213 | Chr17:79916871 |
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TissGeneNet for PYCR1 |
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) |
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TissGeneProg for PYCR1 |
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. |
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. |
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. |
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. |
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TissGeneClin for PYCR1 |
TissGeneDrug for PYCR1 |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
DB00172 | L-Proline | Small molecule | Approved|Nutraceutical |
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TissGeneDisease for PYCR1 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C2751987 | Cutis Laxa, Autosomal Recessive, Type IIB | 5 | BeFree,CLINVAR,CTD_human,ORPHANET,UNIPROT |
umls:C0010495 | Cutis Laxa | 3 | BeFree,CTD_human |
umls:C0268351 | Cutis Laxa, Autosomal Recessive, Type I | 3 | BeFree |
umls:C0025362 | Mental Retardation | 2 | BeFree |
umls:C3280799 | CUTIS LAXA, AUTOSOMAL RECESSIVE, TYPE IIIB | 2 | CLINVAR,ORPHANET,UNIPROT |
umls:C0023470 | Myeloid Leukemia | 1 | BeFree |
umls:C0025007 | Measles | 1 | BeFree |
umls:C0033300 | Progeria | 1 | CTD_human |
umls:C0175754 | Agenesis of corpus callosum | 1 | BeFree |
umls:C0376358 | Malignant neoplasm of prostate | 1 | BeFree |
umls:C0431369 | Dysgenesis of corpus callosum | 1 | BeFree |
umls:C0600139 | Prostate carcinoma | 1 | BeFree |
umls:C0872410 | Posturing | 1 | BeFree |
umls:C1704272 | Benign Prostatic Hyperplasia | 1 | BeFree |
umls:C0432255 | Geroderma osteodysplastica | 0 | ORPHANET |