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Gene: PES1 |
Gene summary for PES1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PES1 | Gene ID | 23481 |
| Gene name | pescadillo ribosomal biogenesis factor 1 | |
| Gene Alias | NOP7 | |
| Cytomap | 22q12.2 | |
| Gene Type | protein-coding | GO ID | GO:0000460 | UniProtAcc | O00541 |
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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 |
| 23481 | PES1 | LZE2T | Human | Esophagus | ESCC | 9.83e-05 | 8.98e-01 | 0.082 |
| 23481 | PES1 | LZE4T | Human | Esophagus | ESCC | 1.18e-10 | 2.96e-01 | 0.0811 |
| 23481 | PES1 | LZE7T | Human | Esophagus | ESCC | 2.68e-05 | 6.13e-01 | 0.0667 |
| 23481 | PES1 | LZE8T | Human | Esophagus | ESCC | 1.10e-03 | 2.40e-01 | 0.067 |
| 23481 | PES1 | LZE24T | Human | Esophagus | ESCC | 2.12e-09 | 3.59e-01 | 0.0596 |
| 23481 | PES1 | LZE6T | Human | Esophagus | ESCC | 3.78e-04 | 2.18e-01 | 0.0845 |
| 23481 | PES1 | P1T-E | Human | Esophagus | ESCC | 1.69e-04 | 3.89e-01 | 0.0875 |
| 23481 | PES1 | P2T-E | Human | Esophagus | ESCC | 3.90e-26 | 4.30e-01 | 0.1177 |
| 23481 | PES1 | P4T-E | Human | Esophagus | ESCC | 1.62e-17 | 5.36e-01 | 0.1323 |
| 23481 | PES1 | P5T-E | Human | Esophagus | ESCC | 3.24e-16 | 2.51e-01 | 0.1327 |
| 23481 | PES1 | P8T-E | Human | Esophagus | ESCC | 1.33e-25 | 4.93e-01 | 0.0889 |
| 23481 | PES1 | P9T-E | Human | Esophagus | ESCC | 3.52e-20 | 5.98e-01 | 0.1131 |
| 23481 | PES1 | P10T-E | Human | Esophagus | ESCC | 8.09e-59 | 1.04e+00 | 0.116 |
| 23481 | PES1 | P11T-E | Human | Esophagus | ESCC | 1.34e-11 | 6.81e-01 | 0.1426 |
| 23481 | PES1 | P12T-E | Human | Esophagus | ESCC | 8.52e-36 | 5.40e-01 | 0.1122 |
| 23481 | PES1 | P15T-E | Human | Esophagus | ESCC | 3.35e-27 | 7.33e-01 | 0.1149 |
| 23481 | PES1 | P16T-E | Human | Esophagus | ESCC | 3.77e-38 | 8.25e-01 | 0.1153 |
| 23481 | PES1 | P17T-E | Human | Esophagus | ESCC | 4.56e-07 | 6.66e-01 | 0.1278 |
| 23481 | PES1 | P19T-E | Human | Esophagus | ESCC | 5.15e-08 | 9.21e-01 | 0.1662 |
| 23481 | PES1 | P20T-E | Human | Esophagus | ESCC | 3.68e-13 | 4.30e-01 | 0.1124 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid 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. |
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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:0000463 | Liver | Cirrhotic | maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 9/4634 | 15/18723 | 3.88e-03 | 2.10e-02 | 9 |
| GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
| GO:004225422 | Liver | HCC | ribosome biogenesis | 246/7958 | 299/18723 | 4.99e-46 | 1.58e-42 | 246 |
| GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| GO:001607212 | Liver | HCC | rRNA metabolic process | 193/7958 | 236/18723 | 1.26e-35 | 1.14e-32 | 193 |
| GO:000636421 | Liver | HCC | rRNA processing | 185/7958 | 225/18723 | 8.14e-35 | 6.45e-32 | 185 |
| GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
| GO:004227322 | Liver | HCC | ribosomal large subunit biogenesis | 64/7958 | 72/18723 | 2.31e-16 | 2.03e-14 | 64 |
| GO:000047011 | Liver | HCC | maturation of LSU-rRNA | 26/7958 | 28/18723 | 2.82e-08 | 6.43e-07 | 26 |
| GO:00004601 | Liver | HCC | maturation of 5.8S rRNA | 29/7958 | 35/18723 | 1.12e-06 | 1.66e-05 | 29 |
| GO:00004631 | Liver | HCC | maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 15/7958 | 15/18723 | 2.65e-06 | 3.54e-05 | 15 |
| GO:0000466 | Liver | HCC | maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 19/7958 | 24/18723 | 2.80e-04 | 2.02e-03 | 19 |
| GO:002261320 | Oral cavity | OSCC | ribonucleoprotein complex biogenesis | 333/7305 | 463/18723 | 8.28e-48 | 5.24e-44 | 333 |
| GO:004225420 | Oral cavity | OSCC | ribosome biogenesis | 230/7305 | 299/18723 | 3.22e-41 | 6.80e-38 | 230 |
| GO:000636410 | Oral cavity | OSCC | rRNA processing | 172/7305 | 225/18723 | 1.57e-30 | 1.24e-27 | 172 |
| GO:00344709 | Oral cavity | OSCC | ncRNA processing | 263/7305 | 395/18723 | 4.38e-29 | 2.78e-26 | 263 |
| GO:001607210 | Oral cavity | OSCC | rRNA metabolic process | 176/7305 | 236/18723 | 6.51e-29 | 3.24e-26 | 176 |
| GO:00346605 | Oral cavity | OSCC | ncRNA metabolic process | 296/7305 | 485/18723 | 2.94e-23 | 6.65e-21 | 296 |
| GO:004227320 | Oral cavity | OSCC | ribosomal large subunit biogenesis | 61/7305 | 72/18723 | 1.52e-15 | 1.06e-13 | 61 |
| GO:00004706 | Oral cavity | OSCC | maturation of LSU-rRNA | 26/7305 | 28/18723 | 3.39e-09 | 7.66e-08 | 26 |
| Page: 1 2 3 4 5 |
| 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 |
| PES1 | SNV | Missense_Mutation | rs774125501 | c.643G>A | p.Val215Met | p.V215M | O00541 | protein_coding | deleterious(0.03) | possibly_damaging(0.56) | TCGA-A2-A3XY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | PD |
| PES1 | SNV | Missense_Mutation | c.50N>G | p.Tyr17Cys | p.Y17C | O00541 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PES1 | SNV | Missense_Mutation | c.1453G>A | p.Glu485Lys | p.E485K | O00541 | protein_coding | tolerated(0.48) | benign(0.021) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PES1 | insertion | Nonsense_Mutation | novel | c.281_282insCTTTTAGTAGAGACTGGGTTTCCCCATGTTGGCCAGGCT | p.Lys94delinsAsnPheTerTerArgLeuGlyPheProMetLeuAlaArgLeu | p.K94delinsNF**RLGFPMLARL | O00541 | protein_coding | TCGA-A8-A094-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PES1 | insertion | Frame_Shift_Ins | novel | c.55_56insGAGTCAAAATAAGACTT | p.Thr19ArgfsTer17 | p.T19Rfs*17 | O00541 | protein_coding | TCGA-B6-A0I9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| PES1 | deletion | Frame_Shift_Del | novel | c.480delG | p.Cys161AlafsTer170 | p.C161Afs*170 | O00541 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| PES1 | SNV | Missense_Mutation | rs781772847 | c.673N>A | p.Glu225Lys | p.E225K | O00541 | protein_coding | deleterious(0) | probably_damaging(0.976) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PES1 | SNV | Missense_Mutation | c.1463N>T | p.Ser488Leu | p.S488L | O00541 | protein_coding | tolerated(0.2) | benign(0) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PES1 | SNV | Missense_Mutation | novel | c.1600N>A | p.Arg534Ser | p.R534S | O00541 | protein_coding | deleterious(0) | possibly_damaging(0.908) | TCGA-AA-3939-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| PES1 | SNV | Missense_Mutation | c.1052G>A | p.Gly351Asp | p.G351D | O00541 | protein_coding | deleterious(0.03) | probably_damaging(0.992) | TCGA-AD-6964-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folfox | PD |
| Page: 1 2 3 4 5 6 7 |
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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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