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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GRHPR |
Basic gene info. | Gene symbol | GRHPR |
Gene name | glyoxylate reductase/hydroxypyruvate reductase | |
Synonyms | GLXR|GLYD|PH2 | |
Cytomap | UCSC genome browser: 9q12 | |
Genomic location | chr9 :37422706-37436986 | |
Type of gene | protein-coding | |
RefGenes | NM_012203.1, | |
Ensembl id | ENSG00000137106 | |
Description | glycerate-2-dehydrogenase | |
Modification date | 20141219 | |
dbXrefs | MIM : 604296 | |
HGNC : HGNC | ||
Ensembl : ENSG00000137106 | ||
HPRD : 05052 | ||
Vega : OTTHUMG00000019914 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GRHPR | |
BioGPS: 9380 | ||
Gene Expression Atlas: ENSG00000137106 | ||
The Human Protein Atlas: ENSG00000137106 | ||
Pathway | NCI Pathway Interaction Database: GRHPR | |
KEGG: GRHPR | ||
REACTOME: GRHPR | ||
ConsensusPathDB | ||
Pathway Commons: GRHPR | ||
Metabolism | MetaCyc: GRHPR | |
HUMANCyc: GRHPR | ||
Regulation | Ensembl's Regulation: ENSG00000137106 | |
miRBase: chr9 :37,422,706-37,436,986 | ||
TargetScan: NM_012203 | ||
cisRED: ENSG00000137106 | ||
Context | iHOP: GRHPR | |
cancer metabolism search in PubMed: GRHPR | ||
UCL Cancer Institute: GRHPR | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for GRHPR(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GRHPR |
Familial Cancer Database: GRHPR |
* This gene is included in those cancer gene databases. |
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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_PYRUVATE_METABOLISM KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GRHPR |
MedGen: GRHPR (Human Medical Genetics with Condition) | |
ClinVar: GRHPR | |
Phenotype | MGI: GRHPR (International Mouse Phenotyping Consortium) |
PhenomicDB: GRHPR |
Mutations for GRHPR |
* 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 GRHPR 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 |
CA414232 | GRHPR | 21 | 181 | 9 | 37432653 | 37432813 | PNO1 | 175 | 697 | 2 | 68401890 | 68402413 | |
AI924257 | GRHPR | 5 | 151 | 9 | 37436841 | 37436987 | LCLAT1 | 141 | 546 | 2 | 30670954 | 30671359 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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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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=25) | (# total SNVs=8) |
(# 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 |
chr9:37425986-37425986 | p.K94K | 2 |
chr9:37432100-37432100 | p.P277H | 2 |
chr9:37430615-37430615 | p.E236K | 2 |
chr9:37424938-37424938 | p.S60S | 2 |
chr9:37432009-37432009 | p.D247N | 2 |
chr9:37424882-37424882 | p.A42T | 1 |
chr9:37432011-37432011 | p.D247E | 1 |
chr9:37425945-37425945 | p.M81V | 1 |
chr9:37429767-37429767 | p.Q178* | 1 |
chr9:37424897-37424897 | p.R47* | 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 |   | 4 |   |   |   |   | 1 |   |   | 3 | 1 |   |   |   | 3 | 3 |   | 5 |
# mutation | 1 | 1 |   | 4 |   |   |   |   | 1 |   |   | 3 | 1 |   |   |   | 3 | 3 |   | 5 |
nonsynonymous SNV | 1 | 1 |   | 2 |   |   |   |   | 1 |   |   | 3 | 1 |   |   |   | 2 | 2 |   | 2 |
synonymous SNV |   |   |   | 2 |   |   |   |   |   |   |   |   |   |   |   |   | 1 | 1 |   | 3 |
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 |
chr9:37424918 | p.L58L | 1 |
chr9:37432008 | p.L314Q | 1 |
chr9:37424932 | p.S60S | 1 |
chr9:37432009 | p.H62H | 1 |
chr9:37424938 | p.M81V | 1 |
chr9:37432011 | p.D105H | 1 |
chr9:37424944 | p.L146L | 1 |
chr9:37432012 | p.E190Q | 1 |
chr9:37425945 | p.T202A | 1 |
chr9:37432088 | p.T222T | 1 |
Other DBs for Point Mutations |
Copy Number for GRHPR 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 GRHPR |
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 |
TMEM261,RPP25L,CCDC107,CLPP,CLTA,CREB3,CUEDC2, DCTN3,DGCR6L,EDF1,FIS1,GRHPR,HINT2,NDUFB6, NFKBIL1,NUDT2,PLEKHJ1,PTGES2,STOML2,TESK1,TSSC4 | AKT1S1,BABAM1,C19orf70,CLPP,COPS6,COX4I1,FIS1, GPS1,GRHPR,IDH3G,MRPL24,MRPS11,MRPS18A,NDUFA13, NDUFB7,NDUFB8,PARK7,POLR2I,PSMD4,STOML2,ZNF511 | ||||
APTX,TMEM261,RPP25L,CLTA,COQ4,DCTN3,EXOSC3, FANCG,GRHPR,HINT2,NDUFA8,NDUFB6,NUDT2,PMPCA, RPL35,RPL7A,SIGMAR1,SMU1,STOML2,TOMM5,TRUB2 | ACTR1B,AIP,ARL6IP4,BOLA1,APOPT1,MALSU1,DGCR6L, ERCC1,GRHPR,KLHDC3,PIN1,POLR2I,PPIE,RPL35A, SCNM1,SUPT4H1,THAP3,THAP7,WBP1,WDR83,ZMAT5 |
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 GRHPR |
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 |
DB00145 | glyoxylate reductase/hydroxypyruvate reductase | approved; nutraceutical | Glycine | ||
DB00160 | glyoxylate reductase/hydroxypyruvate reductase | approved; nutraceutical | L-Alanine |
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Cross referenced IDs for GRHPR |
* 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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