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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for UGDH |
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Phenotypic Information for UGDH(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: UGDH |
Familial Cancer Database: UGDH |
* 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_ASCORBATE_AND_ALDARATE_METABOLISM KEGG_STARCH_AND_SUCROSE_METABOLISM KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: UGDH |
MedGen: UGDH (Human Medical Genetics with Condition) | |
ClinVar: UGDH | |
Phenotype | MGI: UGDH (International Mouse Phenotyping Consortium) |
PhenomicDB: UGDH |
Mutations for UGDH |
* 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 UGDH 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 |
BC013053 | CCDC69 | 1 | 2688 | 5 | 150561074 | 150581246 | UGDH | 2686 | 2948 | 4 | 39501148 | 39501410 | |
AW733157 | UGDH | 4 | 363 | 4 | 39501039 | 39501397 | RPL7L1 | 361 | 477 | 6 | 42854332 | 42854448 | |
BF573050 | MAGT1 | 1 | 168 | X | 77083347 | 77083514 | UGDH | 160 | 515 | 4 | 39501054 | 39501409 |
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=33) | (# total SNVs=9) |
(# total SNVs=3) | (# total SNVs=1) |
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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 |
chr4:39515753-39515753 | p.S72fs*18 | 4 |
chr4:39506041-39506041 | p.F420S | 2 |
chr4:39512402-39512402 | p.R115H | 2 |
chr4:39501876-39501877 | p.? | 2 |
chr4:39523018-39523018 | p.E39* | 2 |
chr4:39507281-39507281 | p.A332P | 2 |
chr4:39507293-39507293 | p.D328Y | 2 |
chr4:39505541-39505541 | p.R443H | 1 |
chr4:39512323-39512323 | p.R141R | 1 |
chr4:39515754-39515754 | p.F71L | 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 | 3 | 1 | 1 | 3 |   |   | 3 |   |   |   |   | 7 | 2 | 1 |   |   | 3 | 5 |   | 3 |
# mutation | 3 | 1 | 1 | 4 |   |   | 3 |   |   |   |   | 7 | 2 | 1 |   |   | 3 | 5 |   | 3 |
nonsynonymous SNV | 2 | 1 |   | 3 |   |   | 3 |   |   |   |   | 6 | 2 | 1 |   |   | 1 | 4 |   | 1 |
synonymous SNV | 1 |   | 1 | 1 |   |   |   |   |   |   |   | 1 |   |   |   |   | 2 | 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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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 |
chr4:39506042 | p.E293K,UGDH | 1 |
chr4:39511480 | p.T95N | 1 |
chr4:39515753 | p.R279K,UGDH | 1 |
chr4:39506055 | p.D76N,UGDH | 1 |
chr4:39511522 | p.L255L,UGDH | 1 |
chr4:39523079 | p.S72P,UGDH | 1 |
chr4:39506118 | p.L220L,UGDH | 1 |
chr4:39512009 | p.P18P,UGDH | 1 |
chr4:39523086 | p.S208N,UGDH | 1 |
chr4:39506886 | p.G16V,UGDH | 1 |
Other DBs for Point Mutations |
Copy Number for UGDH 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 UGDH |
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 |
AFF1,SMIM14,CCNG2,DNAL1,ERBB2IP,FNIP1,HCAR1, KIAA0232,FAM214A,LRBA,LRIG1,PDS5A,PTPN13,RBM47, SETD7,SGK3,SLC30A9,SLC38A1,TP53INP1,UBE2K,UGDH | ABAT,AMMECR1,AREG,SMIM14,CYP51A1,ETNK2,GALNT7, GOLM1,GREB1,KCNK6,LRRC6,LINC00160,PDIA3,PDIA3P1, PLEKHB2,RAB11FIP1,SERPINA5,SORD,TMCO3,TUBA3E,UGDH | ||||
C11orf85,ANKUB1,SMIM14,SBSPON,CAMK2D,DNAH11,DPY19L2P4, GUCA1C,IL1RL1,KHDC1L,KRT1,OR10H4,PCDH9,PLGLA, SPANXA2,TMED10,TRIM16L,TRPA1,UGDH,UTS2B,ZNF488 | ABHD5,ACER3,ACTR2,ADH1C,ADORA2B,C12orf49,CA2, EHHADH,ETNK1,FAM107B,FAR2,GJB2,ME2,AP5M1, NRAS,PGGT1B,PPP1R14C,TGFA,UGDH,UGT1A10,UGT1A8 |
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 UGDH |
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 | UDP-glucose 6-dehydrogenase | approved; nutraceutical | NADH | ||
DB01713 | UDP-glucose 6-dehydrogenase | experimental | Udp-Alpha-D-Xylopyranose | ||
DB01907 | UDP-glucose 6-dehydrogenase | experimental | Nicotinamide-Adenine-Dinucleotide | ||
DB03041 | UDP-glucose 6-dehydrogenase | experimental | Udp-Glucuronic Acid |
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Cross referenced IDs for UGDH |
* 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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