TissGeneSummary for GLDC |
Gene summary |
Basic gene information | Gene symbol | GLDC |
Gene name | glycine dehydrogenase (decarboxylating) | |
Synonyms | GCE|GCSP|HYGN1 | |
Cytomap | UCSC genome browser: 9p22 | |
Type of gene | protein-coding | |
RefGenes | NM_000170.2, | |
Description | glycine cleavage system protein Pglycine decarboxylase P-proteinglycine dehydrogenase (aminomethyl-transferring)glycine dehydrogenase (decarboxylating), mitochondrialglycine dehydrogenase [decarboxylating], mitochondrial | |
Modification date | 20141219 | |
dbXrefs | MIM : 238300 | |
HGNC : HGNC | ||
Ensembl : ENSG00000178445 | ||
HPRD : 01996 | ||
Vega : OTTHUMG00000019524 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GLDC | |
BioGPS: 2731 | ||
Pathway | NCI Pathway Interaction Database: GLDC | |
KEGG: GLDC | ||
REACTOME: GLDC | ||
Pathway Commons: GLDC | ||
Context | iHOP: GLDC | |
ligand binding site mutation search in PubMed: GLDC | ||
UCL Cancer Institute: GLDC | ||
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) | KidneyLiver | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | KIRC,KIRP,KICHLIHC | |
Reference showing the relevant tissue of GLDC | ||
Description by TissGene annotations |
* 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 |
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TissGeneExp for GLDC |
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 |
LUAD | -1.859172709 | -3.247834778 | 1.388662069 | 1.98E-06 | 6.32E-06 |
KICH | -4.832833606 | 3.283066394 | -8.1159 | 8.62E-15 | 1.65E-13 |
THCA | -2.620416047 | 1.047141581 | -3.667557627 | 1.03E-15 | 1.52E-14 |
KIRC | 0.916746783 | 3.927170394 | -3.010423611 | 1.41E-22 | 1.36E-21 |
PRAD | -1.685843067 | -2.919843067 | 1.234 | 0.0209 | 0.045828669 |
COAD | -3.527929606 | -2.155502683 | -1.372426923 | 0.00222 | 0.005881524 |
LIHC | 3.615044394 | 5.234592394 | -1.619548 | 3.91E-05 | 0.000147689 |
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TissGene-miRNA for GLDC |
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 |
UCS | hsa-miR-30c-5p | MIMAT0000244 | 0.031 | -0.29 | 56 |
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TissGeneMut for GLDC |
TissGeneSNV for GLDC |
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.R362H | LGG | 1 |
p.A627S | UCEC | 1 |
p.M904T | LUAD | 1 |
p.W573R | HNSC | 1 |
p.P647L | READ | 1 |
p.K106E | UCEC | 1 |
p.K272N | BRCA | 1 |
p.T277K | LUAD | 1 |
p.N875Y | LUSC | 1 |
p.L404M | LUSC | 1 |
p.R937H | HNSC | 1 |
p.A204S | STAD | 1 |
p.L296R | STAD | 1 |
p.R630Q | READ | 1 |
p.S748P | LIHC | 1 |
p.S286R | LUAD | 1 |
p.S401Y | BLCA | 1 |
p.T277M | UCEC | 1 |
p.R409W | SKCM | 1 |
p.A85T | SKCM | 1 |
p.G156V | BLCA | 1 |
p.A802V | THYM | 1 |
p.A777T | PRAD | 1 |
p.A408D | STAD | 1 |
p.F434L | UCEC | 1 |
p.R461W | KIRC | 1 |
p.R362C | ESCA | 1 |
p.P1004S | UCEC | 1 |
p.D545Y | CESC | 1 |
p.S401F | BLCA | 1 |
p.G590E | SKCM | 1 |
p.S169P | KIRC | 1 |
p.G309R | KIRC | 1 |
p.S951P | LUAD | 1 |
p.E205K | SKCM | 1 |
p.N150K | COAD | 1 |
p.P1011S | UCEC | 1 |
p.I933F | OV | 1 |
p.Q592H | LUAD | 1 |
p.K871N | PRAD | 1 |
p.E115K | SKCM | 1 |
p.S86N | LGG | 1 |
p.P944L | STAD | 1 |
p.A892T | KICH | 1 |
p.D436H | BLCA | 1 |
p.V322E | LIHC | 1 |
p.D258Y | UCEC | 1 |
p.T244I | SKCM | 1 |
p.L120V | LUAD | 1 |
p.G728R | SKCM | 1 |
p.H550R | HNSC | 1 |
p.R149L | LUAD | 1 |
p.S957P | SKCM | 1 |
p.A389V | STAD | 1 |
p.R988Q | HNSC | 1 |
p.L177I | LUAD | 1 |
p.S493C | BRCA | 1 |
p.Y179H | STAD | 1 |
p.P96T | COAD | 1 |
p.W130* | LUAD | 1 |
p.A204T | COAD | 1 |
p.G798* | STAD | 1 |
p.E478* | UCEC | 1 |
p.A837V | STAD | 1 |
p.V583G | LUAD | 1 |
p.K754R | LUAD | 1 |
p.R739H | COAD | 1 |
p.F519L | UCEC | 1 |
p.A802V | LUSC | 1 |
p.R790W | HNSC | 1 |
p.Q180R | STAD | 1 |
p.P509L | ESCA | 1 |
p.P58S | PAAD | 1 |
p.R368K | LUAD | 1 |
p.Q723H | LUAD | 1 |
p.A631S | COAD | 1 |
p.D482Y | HNSC | 1 |
p.R506T | BLCA | 1 |
p.S814P | UCEC | 1 |
p.P554S | SKCM | 1 |
p.H753Q | PRAD | 1 |
p.A931V | UCEC | 1 |
p.V668L | SKCM | 1 |
p.Q385* | BLCA | 1 |
p.S557F | SKCM | 1 |
p.P584T | LUAD | 1 |
p.H959N | LUAD | 1 |
p.F264L | CESC | 1 |
p.R337X | COAD | 1 |
p.N380Y | LUAD | 1 |
p.Y608C | UCEC | 1 |
p.H284Y | HNSC | 1 |
p.I710M | LUAD | 1 |
p.A454S | LIHC | 1 |
p.A498P | OV | 1 |
p.F870L | BLCA | 1 |
p.G798X | STAD | 1 |
p.T830K | LUSC | 1 |
p.R461W | GBM | 1 |
p.R373W | UCEC | 1 |
p.T187I | LUAD | 1 |
p.R373Q | UCEC | 1 |
p.Q587* | HNSC | 1 |
p.K106Q | UCEC | 1 |
p.W573R | UCEC | 1 |
p.V476A | PAAD | 1 |
p.D742Y | UCEC | 1 |
p.L263F | LUAD | 1 |
p.P972S | SKCM | 1 |
p.S492L | BLCA | 1 |
p.T698A | COAD | 1 |
p.P554L | SKCM | 1 |
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TissGeneCNV for GLDC |
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 GLDC |
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-EW-A3U0-01A | RFX3-GLDC | 5UTR-CDS | Chr9:3525747 | Chr9:6565429 |
TCGAfusionPortal | PRADA | HNSC | TCGA-HD-7229-01A | JAK2-GLDC | In-frame | Chr9:5029906 | Chr9:6565429 |
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TissGeneNet for GLDC |
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 GLDC |
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 GLDC |
TissGeneDrug for GLDC |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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TissGeneDisease for GLDC |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0751748 | Nonketotic Hyperglycinemia | 29 | BeFree,CLINVAR,CTD_human,GAD,LHGDN,UNIPROT |
umls:C0003873 | Rheumatoid Arthritis | 1 | BeFree |
umls:C0004352 | Autistic Disorder | 1 | BeFree |
umls:C0007131 | Non-Small Cell Lung Carcinoma | 1 | BeFree |
umls:C0020456 | Hyperglycemia | 1 | LHGDN |
umls:C0024299 | Lymphoma | 1 | BeFree |
umls:C0026827 | Muscle hypotonia | 1 | LHGDN |
umls:C0085583 | Choreoathetosis | 1 | BeFree |
umls:C0149654 | Conduct Disorder | 1 | BeFree |
umls:C0242379 | Malignant neoplasm of lung | 1 | BeFree |
umls:C0265428 | Chromosome 9, partial trisomy 9p | 1 | BeFree |
umls:C0268560 | Hyperglycinemia, Transient Neonatal | 1 | BeFree |
umls:C0346429 | Multiple malignancy | 1 | BeFree |
umls:C0554985 | Aggressive outburst | 1 | BeFree |
umls:C0596263 | Carcinogenesis | 1 | BeFree |
umls:C0684249 | Carcinoma of lung | 1 | BeFree |
umls:C0740409 | Psychotic behaviour | 1 | BeFree |
umls:C0751265 | Learning Disabilities | 1 | BeFree |
umls:C3714756 | Intellectual Disability | 1 | LHGDN |