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Gene: PPP4R1 |
Gene summary for PPP4R1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PPP4R1 | Gene ID | 9989 |
| Gene name | protein phosphatase 4 regulatory subunit 1 | |
| Gene Alias | MEG1 | |
| Cytomap | 18p11.22 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q8TF05 |
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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 |
| 9989 | PPP4R1 | P42T-E | Human | Esophagus | ESCC | 1.93e-08 | 4.20e-01 | 0.1175 |
| 9989 | PPP4R1 | P44T-E | Human | Esophagus | ESCC | 1.39e-03 | 1.58e-01 | 0.1096 |
| 9989 | PPP4R1 | P47T-E | Human | Esophagus | ESCC | 1.75e-10 | 1.28e-01 | 0.1067 |
| 9989 | PPP4R1 | P48T-E | Human | Esophagus | ESCC | 7.78e-14 | 2.83e-01 | 0.0959 |
| 9989 | PPP4R1 | P52T-E | Human | Esophagus | ESCC | 1.89e-21 | 4.95e-01 | 0.1555 |
| 9989 | PPP4R1 | P54T-E | Human | Esophagus | ESCC | 5.92e-15 | 4.24e-01 | 0.0975 |
| 9989 | PPP4R1 | P56T-E | Human | Esophagus | ESCC | 9.30e-05 | 2.42e-01 | 0.1613 |
| 9989 | PPP4R1 | P57T-E | Human | Esophagus | ESCC | 3.88e-10 | 1.01e-01 | 0.0926 |
| 9989 | PPP4R1 | P61T-E | Human | Esophagus | ESCC | 9.96e-17 | -1.80e-02 | 0.099 |
| 9989 | PPP4R1 | P62T-E | Human | Esophagus | ESCC | 8.10e-46 | 1.05e+00 | 0.1302 |
| 9989 | PPP4R1 | P65T-E | Human | Esophagus | ESCC | 5.32e-14 | 3.99e-01 | 0.0978 |
| 9989 | PPP4R1 | P74T-E | Human | Esophagus | ESCC | 4.41e-15 | 5.88e-01 | 0.1479 |
| 9989 | PPP4R1 | P75T-E | Human | Esophagus | ESCC | 4.20e-24 | 4.74e-01 | 0.1125 |
| 9989 | PPP4R1 | P76T-E | Human | Esophagus | ESCC | 3.82e-13 | -6.60e-02 | 0.1207 |
| 9989 | PPP4R1 | P79T-E | Human | Esophagus | ESCC | 3.43e-09 | 3.89e-02 | 0.1154 |
| 9989 | PPP4R1 | P80T-E | Human | Esophagus | ESCC | 1.35e-17 | 7.48e-01 | 0.155 |
| 9989 | PPP4R1 | P83T-E | Human | Esophagus | ESCC | 3.33e-11 | 5.67e-01 | 0.1738 |
| 9989 | PPP4R1 | P84T-E | Human | Esophagus | ESCC | 2.58e-06 | 6.85e-01 | 0.0933 |
| 9989 | PPP4R1 | P89T-E | Human | Esophagus | ESCC | 4.68e-08 | 7.27e-01 | 0.1752 |
| 9989 | PPP4R1 | P91T-E | Human | Esophagus | ESCC | 6.03e-07 | 1.09e+00 | 0.1828 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00064708 | Cervix | CC | protein dephosphorylation | 60/2311 | 281/18723 | 1.33e-05 | 2.68e-04 | 60 |
| GO:00163117 | Cervix | CC | dephosphorylation | 73/2311 | 417/18723 | 1.23e-03 | 9.87e-03 | 73 |
| GO:000647017 | Esophagus | HGIN | protein dephosphorylation | 61/2587 | 281/18723 | 1.86e-04 | 3.51e-03 | 61 |
| GO:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
| GO:000647018 | Esophagus | ESCC | protein dephosphorylation | 177/8552 | 281/18723 | 3.13e-09 | 6.72e-08 | 177 |
| GO:001631121 | Liver | HCC | dephosphorylation | 230/7958 | 417/18723 | 1.00e-07 | 1.96e-06 | 230 |
| GO:000647021 | Liver | HCC | protein dephosphorylation | 162/7958 | 281/18723 | 1.91e-07 | 3.46e-06 | 162 |
| GO:00064707 | Lung | IAC | protein dephosphorylation | 60/2061 | 281/18723 | 3.24e-07 | 2.48e-05 | 60 |
| GO:00163116 | Lung | IAC | dephosphorylation | 75/2061 | 417/18723 | 1.21e-05 | 3.64e-04 | 75 |
| GO:000647012 | Lung | AIS | protein dephosphorylation | 56/1849 | 281/18723 | 2.47e-07 | 2.24e-05 | 56 |
| GO:001631112 | Lung | AIS | dephosphorylation | 69/1849 | 417/18723 | 1.27e-05 | 4.78e-04 | 69 |
| GO:000647022 | Lung | AAH | protein dephosphorylation | 21/613 | 281/18723 | 4.01e-04 | 1.78e-02 | 21 |
| GO:000647015 | Oral cavity | OSCC | protein dephosphorylation | 162/7305 | 281/18723 | 1.56e-10 | 4.56e-09 | 162 |
| GO:00163119 | Oral cavity | OSCC | dephosphorylation | 220/7305 | 417/18723 | 6.33e-09 | 1.34e-07 | 220 |
| GO:000647010 | Prostate | BPH | protein dephosphorylation | 78/3107 | 281/18723 | 1.53e-06 | 2.63e-05 | 78 |
| GO:00163118 | Prostate | BPH | dephosphorylation | 98/3107 | 417/18723 | 1.53e-04 | 1.35e-03 | 98 |
| GO:000647014 | Prostate | Tumor | protein dephosphorylation | 76/3246 | 281/18723 | 2.86e-05 | 3.46e-04 | 76 |
| GO:001631113 | Prostate | Tumor | dephosphorylation | 98/3246 | 417/18723 | 7.31e-04 | 5.08e-03 | 98 |
| GO:000647019 | Skin | AK | protein dephosphorylation | 49/1910 | 281/18723 | 1.30e-04 | 1.61e-03 | 49 |
| GO:0006470110 | Skin | SCCIS | protein dephosphorylation | 25/919 | 281/18723 | 3.08e-03 | 2.80e-02 | 25 |
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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 |
| PPP4R1 | insertion | Frame_Shift_Ins | novel | c.2478_2479insTCAGCCTACACCCCAAGTACAATACTTCTGGATTCTGTTT | p.Glu827SerfsTer14 | p.E827Sfs*14 | Q8TF05 | protein_coding | TCGA-AN-A0FW-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| PPP4R1 | insertion | Frame_Shift_Ins | novel | c.1643_1644insCTCCAAAA | p.Glu549SerfsTer15 | p.E549Sfs*15 | Q8TF05 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PPP4R1 | deletion | Frame_Shift_Del | novel | c.2164delN | p.Lys723AsnfsTer7 | p.K723Nfs*7 | Q8TF05 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| PPP4R1 | deletion | Frame_Shift_Del | novel | c.1107delN | p.Leu370SerfsTer26 | p.L370Sfs*26 | Q8TF05 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| PPP4R1 | SNV | Missense_Mutation | c.2596N>G | p.Leu866Val | p.L866V | Q8TF05 | protein_coding | tolerated(0.16) | benign(0.071) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| PPP4R1 | SNV | Missense_Mutation | c.1791N>C | p.Leu597Phe | p.L597F | Q8TF05 | protein_coding | tolerated(0.06) | benign(0.379) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| PPP4R1 | SNV | Missense_Mutation | c.1791N>C | p.Leu597Phe | p.L597F | Q8TF05 | protein_coding | tolerated(0.06) | benign(0.379) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PPP4R1 | deletion | Frame_Shift_Del | novel | c.2243delN | p.Leu748TrpfsTer2 | p.L748Wfs*2 | Q8TF05 | protein_coding | TCGA-DS-A7WH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | ||
| PPP4R1 | SNV | Missense_Mutation | novel | c.1202N>A | p.Pro401Gln | p.P401Q | Q8TF05 | protein_coding | tolerated(0.24) | benign(0) | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| PPP4R1 | SNV | Missense_Mutation | c.2210N>T | p.Arg737Ile | p.R737I | Q8TF05 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | 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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