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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GNPDA1 |
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Phenotypic Information for GNPDA1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GNPDA1 |
Familial Cancer Database: GNPDA1 |
* 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_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GNPDA1 |
MedGen: GNPDA1 (Human Medical Genetics with Condition) | |
ClinVar: GNPDA1 | |
Phenotype | MGI: GNPDA1 (International Mouse Phenotyping Consortium) |
PhenomicDB: GNPDA1 |
Mutations for GNPDA1 |
* 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 GNPDA1 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 |
N45950 | GNPDA1 | 1 | 79 | 5 | 141380562 | 141380640 | GNPDA1 | 75 | 363 | 5 | 141380253 | 141380539 | |
BU619601 | GNPDA1 | 13 | 201 | 5 | 141380236 | 141382699 | GNPDA1 | 196 | 579 | 5 | 141381388 | 141382729 | |
BU618872 | GNPDA1 | 13 | 200 | 5 | 141380236 | 141382699 | GNPDA1 | 195 | 578 | 5 | 141381388 | 141382729 | |
AA383455 | GNPDA1 | 13 | 98 | 5 | 141380559 | 141380644 | PPP2R2B | 95 | 115 | 5 | 146299111 | 146299131 | |
W00428 | GNPDA1 | 2 | 82 | 5 | 141380560 | 141380640 | GNPDA1 | 78 | 377 | 5 | 141380241 | 141380539 | |
BE162856 | KLHL10 | 187 | 206 | 17 | 40001320 | 40001339 | GNPDA1 | 194 | 329 | 5 | 141380648 | 141380783 |
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=11) | (# total SNVs=3) |
(# total SNVs=2) | (# 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 |
chr5:141391532-141391532 | p.R23R | 3 |
chr5:141385882-141385882 | p.R79Q | 2 |
chr5:141384531-141384531 | p.T187M | 2 |
chr5:141391505-141391505 | p.E32D | 2 |
chr5:141391553-141391553 | p.A16A | 1 |
chr5:141381655-141381655 | p.Y270C | 1 |
chr5:141385781-141385781 | p.D113N | 1 |
chr5:141391557-141391557 | p.W15L | 1 |
chr5:141381656-141381656 | p.Y270H | 1 |
chr5:141385836-141385838 | p.F94delF | 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 |   |   |   | 2 |   |   | 1 |   | 1 |   |   | 2 |   |   |   |   | 1 | 3 |   | 3 |
# mutation |   |   |   | 2 |   |   | 1 |   | 1 |   |   | 2 |   |   |   |   | 1 | 3 |   | 2 |
nonsynonymous SNV |   |   |   | 2 |   |   | 1 |   | 1 |   |   | 2 |   |   |   |   |   | 3 |   | 2 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   | 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 |
chr5:141391505 | p.E32D | 2 |
chr5:141381655 | p.R158C | 1 |
chr5:141391485 | p.T157T | 1 |
chr5:141381656 | p.G139C | 1 |
chr5:141382753 | p.G136A | 1 |
chr5:141384619 | p.C118Y | 1 |
chr5:141384620 | p.D113N | 1 |
chr5:141384676 | p.R79Q | 1 |
chr5:141385711 | p.K67N | 1 |
chr5:141385765 | p.L39H | 1 |
Other DBs for Point Mutations |
Copy Number for GNPDA1 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 GNPDA1 |
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 |
ATP6V1C1,CCDC43,CDC23,FAM114A2,GEMIN5,GNPDA1,H2AFY, HARS2,HSPA9,LARS,MRPS27,NDFIP1,PAIP2,PPP2CA, RAD17,RBM22,RNF14,SNX24,TMEM67,VDAC1,ZMAT2 | AIF1,ARPC5,ARRB2,C1orf162,C1orf85,C1QB,CD33, CHST13,FCER1G,FUCA1,GNPDA1,GSTO1,LGALS9,LST1, NAGA,NLRC4,NPC2,RNASE6,SLC7A7,STMN1,TNFAIP8L2 | ||||
ABCF2,AHCY,ATP5E,ATP6V1F,COPRS,C20orf24,MALSU1, CDK5,EIF2S2,GNPDA1,HDAC3,MRPS23,NIT2,PDRG1, PDZD11,PSMA7,PSMB3,RAE1,ROMO1,TP53RK,UQCC1 | ALDH1A1,ATP6V1B2,CISD1,CUTC,CYB5A,DKFZp779M0652,FTL, GATM,GNPDA1,LMO4,NINJ1,PFN2,RWDD2A,SCPEP1, SIRT2,SIRT4,SNX2,STOML1,VKORC1,ZBTB14,ZNF16 |
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 GNPDA1 |
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 |
DB02379 | glucosamine-6-phosphate deaminase 1 | experimental | Beta-D-Glucose | ||
DB02445 | glucosamine-6-phosphate deaminase 1 | experimental | 2-Deoxy-2-Amino Glucitol-6-Phosphate | ||
DB03951 | glucosamine-6-phosphate deaminase 1 | experimental | 16g |
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Cross referenced IDs for GNPDA1 |
* 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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