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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PYCR2 |
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Phenotypic Information for PYCR2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PYCR2 |
Familial Cancer Database: PYCR2 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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_ARGININE_AND_PROLINE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PYCR2 |
MedGen: PYCR2 (Human Medical Genetics with Condition) | |
ClinVar: PYCR2 | |
Phenotype | MGI: PYCR2 (International Mouse Phenotyping Consortium) |
PhenomicDB: PYCR2 |
Mutations for PYCR2 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PYCR2 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 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=14) | (# total SNVs=4) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr1:226110046-226110046 | p.T59M | 2 |
chr1:226108200-226108200 | p.G306G | 2 |
chr1:226109705-226109705 | p.G131G | 2 |
chr1:226108290-226108290 | p.K276N | 1 |
chr1:226109762-226109762 | p.Q112H | 1 |
chr1:226109030-226109030 | p.C225C | 1 |
chr1:226109959-226109959 | p.A88G | 1 |
chr1:226109261-226109261 | p.Q208H | 1 |
chr1:226109987-226109987 | p.L79V | 1 |
chr1:226109287-226109287 | p.R200C | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   | 1 |   |   |   |   |   |   | 1 | 1 |   | 5 |   |   |   |   | 1 | 2 |   | 2 |
# mutation |   | 1 |   |   |   |   |   |   | 1 | 1 |   | 5 |   |   |   |   | 1 | 2 |   | 2 |
nonsynonymous SNV |   | 1 |   |   |   |   |   |   | 1 | 1 |   | 5 |   |   |   |   | 1 | 1 |   | 2 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 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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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 |
chr1:226108984 | p.Q134Q,PYCR2 | 1 |
chr1:226109261 | p.A113V,PYCR2 | 1 |
chr1:226109325 | p.E164D | 1 |
chr1:226109606 | p.E163Q | 1 |
chr1:226109611 | p.Q147H | 1 |
chr1:226109657 | p.V143L | 1 |
chr1:226109671 | p.A132T | 1 |
chr1:226109704 | p.Q112H | 1 |
chr1:226109762 | p.H62N,PYCR2 | 1 |
chr1:226108231 | p.M48V,PYCR2 | 1 |
Other DBs for Point Mutations |
Copy Number for PYCR2 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 PYCR2 |
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. |
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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 |
APOA1BP,ARF1,C16orf13,C1orf35,C1orf56,NTPCR,RRNAD1, JTB,MRPL24,MRPL55,MTX1,NENF,PSEN2,PYCR2, RNF187,LAMTOR2,PAM16,TMEM9,TRIM11,TSTD1,ZNF692 | ACTR1B,ADRM1,RABL6,CCDC22,CDC37,CHMP6,NELFB, CUEDC2,GADD45GIP1,GPKOW,MAP2K2,MBD3,MCRS1,MRPL28, NCAPH2,PYCR2,SIVA1,SSNA1,STK11,THAP4,TMED1 | ||||
ACBD6,B4GALT3,C1orf35,CLK2,DAP3,FLAD1,MRPL24, MRPL55,NVL,PFDN2,PPOX,PSMD4,PYCR2,PYGO2, RNF187,SCAMP3,SETDB1,TARS2,UBE2Q1,UBQLN4,USP21 | ARMCX3,C11orf84,CCDC124,COQ10A,CWC27,DCPS,DEF8, DYX1C1,MARS,PHKA1,POLR3H,PRPS1,PYCR2,RAD51D, SLC36A4,SRP68,TRMT61A,TSR1,TUBG1,UPF3B,XPOT |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for PYCR2 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00157 | pyrroline-5-carboxylate reductase family, member 2 | approved; nutraceutical | NADH | ||
DB00172 | pyrroline-5-carboxylate reductase family, member 2 | approved; nutraceutical | L-Proline |
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Cross referenced IDs for PYCR2 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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