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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GNPDA2 |
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Phenotypic Information for GNPDA2(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: GNPDA2 |
Familial Cancer Database: GNPDA2 |
* 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/ |
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KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: GNPDA2 |
MedGen: GNPDA2 (Human Medical Genetics with Condition) | |
ClinVar: GNPDA2 | |
Phenotype | MGI: GNPDA2 (International Mouse Phenotyping Consortium) |
PhenomicDB: GNPDA2 |
Mutations for GNPDA2 |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GNPDA2 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 |
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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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Stat. for Non-Synonymous SNVs (# total SNVs=23) | (# total SNVs=5) |
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(# total SNVs=1) | (# total SNVs=0) |
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* 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 |
chr4:44709820-44709820 | p.D240N | 2 |
chr4:44713015-44713015 | p.T183T | 2 |
chr4:44709886-44709886 | p.E218* | 1 |
chr4:44713035-44713035 | p.D177Y | 1 |
chr4:44719247-44719247 | p.D98N | 1 |
chr4:44709924-44709924 | p.G205E | 1 |
chr4:44713069-44713069 | p.D165E | 1 |
chr4:44719279-44719279 | p.S87F | 1 |
chr4:44709931-44709931 | p.I203V | 1 |
chr4:44713078-44713078 | p.L162L | 1 |
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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 |   |   |   |   |   |   |   | 4 | 3 |   |   |   | 2 | 3 |   | 6 |
# mutation | 1 | 1 |   | 4 |   |   |   |   |   |   |   | 4 | 3 |   |   |   | 2 | 3 |   | 8 |
nonsynonymous SNV |   | 1 |   | 3 |   |   |   |   |   |   |   | 3 | 2 |   |   |   |   | 3 |   | 8 |
synonymous SNV | 1 |   |   | 1 |   |   |   |   |   |   |   | 1 | 1 |   |   |   | 2 |   |   |   |
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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* 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 |
chr4:44709820 | p.D206N,GNPDA2 | 2 |
chr4:44712982 | p.L144S,GNPDA2 | 1 |
chr4:44719247 | p.D143Y,GNPDA2 | 1 |
chr4:44712985 | p.D131E,GNPDA2 | 1 |
chr4:44720403 | p.L128L,GNPDA2 | 1 |
chr4:44713010 | p.T123A,GNPDA2 | 1 |
chr4:44720409 | p.K92K,GNPDA2 | 1 |
chr4:44705105 | p.G241V,GNPDA2 | 1 |
chr4:44713031 | p.K92R,GNPDA2 | 1 |
chr4:44724108 | p.F236F,GNPDA2 | 1 |
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* 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. |
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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 GNPDA2 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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BOD1L1,C5orf24,CDK17,CSNK1G3,DMXL1,FBXL5,GNPDA2, GUF1,HAUS3,CFAP97,MBLAC2,PDS5A,PLA2G12A,PREPL, SCAMP1,SEPSECS,SLC30A9,TRIM23,UBE2K,WDR19,ZNF721 | ANKRD13C,C16orf52,CAPN7,CGGBP1,FAM8A1,FBXO28,GNPDA2, LANCL1,LRRC40,MIER1,MTMR6,NAPG,NSL1,PCNP, RAB5A,SEPT10,TM9SF3,TRAPPC6B,TROVE2,UFM1,VAMP4 |
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BBS10,BMI1,C5orf24,CCDC91,CREG1,DUSP19,FAM200B, GABPA,GLIPR1L2,GNPDA2,KBTBD3,LIAS,PACRGL,PIGY, RAB28,TBC1D19,TIPRL,TMEM128,TMEM55A,UBE2K,VAMP4 | ARPP19,ATL2,C9orf3,CETN2,CFL2,CLIC4,DNAJC24, DPT,MICU3,EID1,ZC2HC1A,COX20,GNG11,GNPDA2, HIAT1,SCHIP1,SEPT7,TCEAL1,TCEAL7,ZNF25,ZNF781 |
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* 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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Pharmacological Information for GNPDA2 |
There's no related Drug. |
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Cross referenced IDs for GNPDA2 |
* 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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