|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: URAD |
Gene summary for URAD |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | URAD | Gene ID | 646625 |
| Gene name | ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5-) decarboxylase | |
| Gene Alias | PRHOXNB | |
| Cytomap | 13q12.2 | |
| Gene Type | protein-coding | GO ID | GO:0000255 | UniProtAcc | A6NGE7 |
Top |
Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 646625 | URAD | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.42e-04 | 2.49e-01 | -0.1808 |
| 646625 | URAD | HTA11_78_2000001011 | Human | Colorectum | AD | 1.05e-04 | 3.38e-01 | -0.1088 |
| 646625 | URAD | HTA11_347_2000001011 | Human | Colorectum | AD | 1.27e-17 | 5.01e-01 | -0.1954 |
| 646625 | URAD | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.30e-04 | 3.22e-01 | -0.1207 |
| 646625 | URAD | HTA11_83_2000001011 | Human | Colorectum | SER | 1.21e-06 | 4.43e-01 | -0.1526 |
| 646625 | URAD | HTA11_696_2000001011 | Human | Colorectum | AD | 5.57e-14 | 4.47e-01 | -0.1464 |
| 646625 | URAD | HTA11_866_2000001011 | Human | Colorectum | AD | 1.07e-07 | 2.96e-01 | -0.1001 |
| 646625 | URAD | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.70e-06 | 3.27e-01 | -0.059 |
| 646625 | URAD | HTA11_5216_2000001011 | Human | Colorectum | SER | 1.59e-03 | 4.23e-01 | -0.1462 |
| 646625 | URAD | HTA11_546_2000001011 | Human | Colorectum | AD | 2.98e-05 | 3.88e-01 | -0.0842 |
| 646625 | URAD | HTA11_7862_2000001011 | Human | Colorectum | AD | 2.26e-03 | 3.38e-01 | -0.0179 |
| 646625 | URAD | HTA11_7663_2000001011 | Human | Colorectum | SER | 3.22e-02 | 4.10e-01 | 0.0131 |
| 646625 | URAD | HTA11_6801_2000001011 | Human | Colorectum | SER | 1.97e-02 | 5.30e-01 | 0.0171 |
| 646625 | URAD | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.75e-03 | 2.96e-01 | 0.0338 |
| 646625 | URAD | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.53e-08 | 3.47e-01 | 0.0674 |
| 646625 | URAD | HTA11_7469_2000001011 | Human | Colorectum | AD | 2.87e-08 | 9.86e-01 | -0.0124 |
| 646625 | URAD | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.86e-02 | 2.07e-01 | 0.3005 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
Top |
Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0072521 | Colorectum | AD | purine-containing compound metabolic process | 153/3918 | 416/18723 | 4.34e-14 | 1.01e-11 | 153 |
| GO:0044282 | Colorectum | AD | small molecule catabolic process | 118/3918 | 376/18723 | 1.05e-06 | 3.55e-05 | 118 |
| GO:00725211 | Colorectum | SER | purine-containing compound metabolic process | 113/2897 | 416/18723 | 4.80e-10 | 5.68e-08 | 113 |
| GO:00442821 | Colorectum | SER | small molecule catabolic process | 87/2897 | 376/18723 | 5.31e-05 | 1.27e-03 | 87 |
| GO:00725212 | Colorectum | MSS | purine-containing compound metabolic process | 132/3467 | 416/18723 | 4.13e-11 | 4.86e-09 | 132 |
| GO:00442822 | Colorectum | MSS | small molecule catabolic process | 94/3467 | 376/18723 | 9.85e-04 | 9.86e-03 | 94 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
Top |
Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
Top |
Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| URAD | SNV | Missense_Mutation | rs775192997 | c.31C>A | p.Leu11Ile | p.L11I | A6NGE7 | protein_coding | deleterious(0.04) | benign(0.012) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| URAD | SNV | Missense_Mutation | c.67N>C | p.Glu23Gln | p.E23Q | A6NGE7 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-FU-A3YQ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| URAD | SNV | Missense_Mutation | c.62C>T | p.Ala21Val | p.A21V | A6NGE7 | protein_coding | tolerated(1) | benign(0) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| URAD | SNV | Missense_Mutation | c.71N>T | p.Arg24Ile | p.R24I | A6NGE7 | protein_coding | deleterious(0.02) | benign(0.328) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR | |
| URAD | SNV | Missense_Mutation | rs780477671 | c.83N>C | p.Ile28Thr | p.I28T | A6NGE7 | protein_coding | deleterious(0.02) | possibly_damaging(0.49) | TCGA-AJ-A3BG-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | PD |
| URAD | SNV | Missense_Mutation | novel | c.100T>A | p.Ser34Thr | p.S34T | A6NGE7 | protein_coding | tolerated(0.08) | benign(0.157) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| URAD | SNV | Missense_Mutation | novel | c.23N>A | p.Ser8Tyr | p.S8Y | A6NGE7 | protein_coding | deleterious(0.02) | probably_damaging(0.949) | TCGA-BS-A0UF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| URAD | SNV | Missense_Mutation | novel | c.135N>T | p.Glu45Asp | p.E45D | A6NGE7 | protein_coding | tolerated(0.08) | benign(0.015) | TCGA-D1-A16X-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| URAD | SNV | Missense_Mutation | c.91N>T | p.Ala31Ser | p.A31S | A6NGE7 | protein_coding | deleterious(0.04) | possibly_damaging(0.871) | TCGA-55-8514-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| URAD | SNV | Missense_Mutation | novel | c.101N>T | p.Ser34Phe | p.S34F | A6NGE7 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-CV-7568-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 |
Top |
Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |