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Gene: PUDP |
Gene summary for PUDP |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PUDP | Gene ID | 8226 |
| Gene name | pseudouridine 5'-phosphatase | |
| Gene Alias | DXF68S1E | |
| Cytomap | Xp22.31 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q08623 |
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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 |
| 8226 | PUDP | LZE4T | Human | Esophagus | ESCC | 2.33e-05 | 1.96e-01 | 0.0811 |
| 8226 | PUDP | LZE8T | Human | Esophagus | ESCC | 2.41e-02 | 1.39e-01 | 0.067 |
| 8226 | PUDP | LZE20T | Human | Esophagus | ESCC | 1.96e-03 | 1.25e-01 | 0.0662 |
| 8226 | PUDP | LZE22T | Human | Esophagus | ESCC | 1.25e-02 | 3.46e-01 | 0.068 |
| 8226 | PUDP | LZE24T | Human | Esophagus | ESCC | 1.77e-04 | 1.40e-01 | 0.0596 |
| 8226 | PUDP | P2T-E | Human | Esophagus | ESCC | 2.76e-23 | 3.86e-01 | 0.1177 |
| 8226 | PUDP | P4T-E | Human | Esophagus | ESCC | 1.14e-10 | 2.87e-01 | 0.1323 |
| 8226 | PUDP | P5T-E | Human | Esophagus | ESCC | 2.09e-04 | 8.00e-02 | 0.1327 |
| 8226 | PUDP | P8T-E | Human | Esophagus | ESCC | 6.99e-38 | 7.08e-01 | 0.0889 |
| 8226 | PUDP | P10T-E | Human | Esophagus | ESCC | 4.24e-07 | 1.18e-01 | 0.116 |
| 8226 | PUDP | P12T-E | Human | Esophagus | ESCC | 8.76e-15 | 2.86e-01 | 0.1122 |
| 8226 | PUDP | P15T-E | Human | Esophagus | ESCC | 1.53e-07 | 1.86e-01 | 0.1149 |
| 8226 | PUDP | P16T-E | Human | Esophagus | ESCC | 2.06e-15 | 1.39e-01 | 0.1153 |
| 8226 | PUDP | P20T-E | Human | Esophagus | ESCC | 1.18e-05 | 1.42e-01 | 0.1124 |
| 8226 | PUDP | P21T-E | Human | Esophagus | ESCC | 1.84e-07 | 1.17e-01 | 0.1617 |
| 8226 | PUDP | P23T-E | Human | Esophagus | ESCC | 4.90e-05 | 9.41e-02 | 0.108 |
| 8226 | PUDP | P24T-E | Human | Esophagus | ESCC | 6.23e-03 | 7.87e-02 | 0.1287 |
| 8226 | PUDP | P26T-E | Human | Esophagus | ESCC | 4.36e-10 | 2.23e-01 | 0.1276 |
| 8226 | PUDP | P27T-E | Human | Esophagus | ESCC | 1.51e-07 | 1.72e-01 | 0.1055 |
| 8226 | PUDP | P28T-E | Human | Esophagus | ESCC | 4.33e-08 | 1.69e-01 | 0.1149 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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. |
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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:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
| GO:0006753110 | Esophagus | ESCC | nucleoside phosphate metabolic process | 288/8552 | 497/18723 | 1.80e-08 | 3.50e-07 | 288 |
| GO:0009117111 | Esophagus | ESCC | nucleotide metabolic process | 282/8552 | 489/18723 | 4.70e-08 | 8.50e-07 | 282 |
| GO:00163116 | Lung | IAC | dephosphorylation | 75/2061 | 417/18723 | 1.21e-05 | 3.64e-04 | 75 |
| GO:001631112 | Lung | AIS | dephosphorylation | 69/1849 | 417/18723 | 1.27e-05 | 4.78e-04 | 69 |
| GO:00163119 | Oral cavity | OSCC | dephosphorylation | 220/7305 | 417/18723 | 6.33e-09 | 1.34e-07 | 220 |
| GO:000675318 | Oral cavity | OSCC | nucleoside phosphate metabolic process | 247/7305 | 497/18723 | 6.28e-07 | 8.96e-06 | 247 |
| GO:000911719 | Oral cavity | OSCC | nucleotide metabolic process | 243/7305 | 489/18723 | 7.80e-07 | 1.09e-05 | 243 |
| GO:001631114 | Oral cavity | EOLP | dephosphorylation | 85/2218 | 417/18723 | 3.19e-07 | 9.47e-06 | 85 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
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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 |
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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 |
| PUDP | SNV | Missense_Mutation | c.194G>A | p.Ser65Asn | p.S65N | Q08623 | protein_coding | tolerated(0.06) | benign(0.012) | TCGA-A8-A094-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PUDP | insertion | Nonsense_Mutation | novel | c.78_79insAAAGTTTAGGAAATATGCTGCCTGGCCAT | p.Val27LysfsTer3 | p.V27Kfs*3 | Q08623 | protein_coding | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| PUDP | SNV | Missense_Mutation | c.425N>T | p.Ser142Leu | p.S142L | Q08623 | protein_coding | tolerated(0.07) | benign(0.096) | TCGA-C5-A2LS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PUDP | SNV | Missense_Mutation | c.160C>G | p.Gln54Glu | p.Q54E | Q08623 | protein_coding | tolerated(0.6) | benign(0.009) | TCGA-EK-A2PL-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PUDP | SNV | Missense_Mutation | rs778192547 | c.139C>T | p.Arg47Trp | p.R47W | Q08623 | protein_coding | deleterious(0) | benign(0.056) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PUDP | SNV | Missense_Mutation | novel | c.376C>T | p.Arg126Trp | p.R126W | Q08623 | protein_coding | deleterious(0.02) | possibly_damaging(0.497) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PUDP | SNV | Missense_Mutation | c.415N>A | p.Gly139Arg | p.G139R | Q08623 | protein_coding | deleterious(0.04) | benign(0.038) | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | SD | |
| PUDP | SNV | Missense_Mutation | c.125G>T | p.Trp42Leu | p.W42L | Q08623 | protein_coding | tolerated(0.68) | benign(0) | TCGA-G4-6302-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PUDP | SNV | Missense_Mutation | c.459N>A | p.Phe153Leu | p.F153L | Q08623 | protein_coding | tolerated(0.68) | benign(0.003) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| PUDP | SNV | Missense_Mutation | novel | c.494N>G | p.Asp165Gly | p.D165G | Q08623 | protein_coding | deleterious(0) | possibly_damaging(0.903) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
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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 |
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