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Gene: PPP1R3D |
Gene summary for PPP1R3D |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PPP1R3D | Gene ID | 5509 |
| Gene name | protein phosphatase 1 regulatory subunit 3D | |
| Gene Alias | PPP1R6 | |
| Cytomap | 20q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0000271 | UniProtAcc | O95685 |
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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 |
| 5509 | PPP1R3D | P1T-E | Human | Esophagus | ESCC | 2.88e-02 | 1.75e-01 | 0.0875 |
| 5509 | PPP1R3D | P2T-E | Human | Esophagus | ESCC | 4.47e-09 | 1.98e-01 | 0.1177 |
| 5509 | PPP1R3D | P9T-E | Human | Esophagus | ESCC | 4.34e-02 | 9.83e-02 | 0.1131 |
| 5509 | PPP1R3D | P10T-E | Human | Esophagus | ESCC | 1.24e-11 | 2.10e-01 | 0.116 |
| 5509 | PPP1R3D | P12T-E | Human | Esophagus | ESCC | 2.06e-17 | 3.94e-01 | 0.1122 |
| 5509 | PPP1R3D | P15T-E | Human | Esophagus | ESCC | 3.89e-07 | 1.88e-01 | 0.1149 |
| 5509 | PPP1R3D | P16T-E | Human | Esophagus | ESCC | 6.02e-08 | 2.10e-01 | 0.1153 |
| 5509 | PPP1R3D | P20T-E | Human | Esophagus | ESCC | 3.93e-09 | 2.64e-01 | 0.1124 |
| 5509 | PPP1R3D | P21T-E | Human | Esophagus | ESCC | 1.25e-05 | 1.34e-01 | 0.1617 |
| 5509 | PPP1R3D | P22T-E | Human | Esophagus | ESCC | 4.01e-02 | 1.05e-01 | 0.1236 |
| 5509 | PPP1R3D | P23T-E | Human | Esophagus | ESCC | 8.82e-17 | 4.22e-01 | 0.108 |
| 5509 | PPP1R3D | P26T-E | Human | Esophagus | ESCC | 5.26e-21 | 5.49e-01 | 0.1276 |
| 5509 | PPP1R3D | P27T-E | Human | Esophagus | ESCC | 1.22e-03 | 9.20e-02 | 0.1055 |
| 5509 | PPP1R3D | P28T-E | Human | Esophagus | ESCC | 4.85e-08 | 1.95e-01 | 0.1149 |
| 5509 | PPP1R3D | P30T-E | Human | Esophagus | ESCC | 4.87e-04 | 2.46e-01 | 0.137 |
| 5509 | PPP1R3D | P31T-E | Human | Esophagus | ESCC | 2.71e-04 | 1.28e-01 | 0.1251 |
| 5509 | PPP1R3D | P36T-E | Human | Esophagus | ESCC | 2.19e-11 | 4.14e-01 | 0.1187 |
| 5509 | PPP1R3D | P37T-E | Human | Esophagus | ESCC | 1.93e-03 | 1.19e-01 | 0.1371 |
| 5509 | PPP1R3D | P39T-E | Human | Esophagus | ESCC | 5.94e-06 | 1.40e-01 | 0.0894 |
| 5509 | PPP1R3D | P47T-E | Human | Esophagus | ESCC | 4.66e-06 | 1.77e-01 | 0.1067 |
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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 |
| ∗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:0006091110 | Esophagus | ESCC | generation of precursor metabolites and energy | 331/8552 | 490/18723 | 3.86e-23 | 8.45e-21 | 331 |
| GO:0015980110 | Esophagus | ESCC | energy derivation by oxidation of organic compounds | 220/8552 | 318/18723 | 1.20e-17 | 1.09e-15 | 220 |
| 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:00059969 | Esophagus | ESCC | monosaccharide metabolic process | 159/8552 | 257/18723 | 1.11e-07 | 1.81e-06 | 159 |
| GO:00193189 | Esophagus | ESCC | hexose metabolic process | 147/8552 | 237/18723 | 2.63e-07 | 3.94e-06 | 147 |
| GO:00060069 | Esophagus | ESCC | glucose metabolic process | 119/8552 | 196/18723 | 1.51e-05 | 1.36e-04 | 119 |
| GO:004346719 | Esophagus | ESCC | regulation of generation of precursor metabolites and energy | 81/8552 | 130/18723 | 9.58e-05 | 6.81e-04 | 81 |
| GO:00442626 | Esophagus | ESCC | cellular carbohydrate metabolic process | 160/8552 | 283/18723 | 1.43e-04 | 9.66e-04 | 160 |
| GO:00160514 | Esophagus | ESCC | carbohydrate biosynthetic process | 117/8552 | 202/18723 | 2.96e-04 | 1.79e-03 | 117 |
| GO:00620129 | Esophagus | ESCC | regulation of small molecule metabolic process | 184/8552 | 334/18723 | 3.11e-04 | 1.85e-03 | 184 |
| GO:001605216 | Esophagus | ESCC | carbohydrate catabolic process | 91/8552 | 154/18723 | 5.39e-04 | 2.97e-03 | 91 |
| GO:00434713 | Esophagus | ESCC | regulation of cellular carbohydrate catabolic process | 11/8552 | 12/18723 | 1.26e-03 | 6.06e-03 | 11 |
| GO:00109065 | Esophagus | ESCC | regulation of glucose metabolic process | 71/8552 | 119/18723 | 1.46e-03 | 6.92e-03 | 71 |
| GO:00061096 | Esophagus | ESCC | regulation of carbohydrate metabolic process | 101/8552 | 178/18723 | 1.89e-03 | 8.52e-03 | 101 |
| GO:00106755 | Esophagus | ESCC | regulation of cellular carbohydrate metabolic process | 83/8552 | 146/18723 | 4.24e-03 | 1.69e-02 | 83 |
| GO:00442751 | Esophagus | ESCC | cellular carbohydrate catabolic process | 27/8552 | 40/18723 | 4.39e-03 | 1.73e-02 | 27 |
| GO:004347010 | Esophagus | ESCC | regulation of carbohydrate catabolic process | 35/8552 | 56/18723 | 8.30e-03 | 2.94e-02 | 35 |
| GO:00346372 | Esophagus | ESCC | cellular carbohydrate biosynthetic process | 46/8552 | 78/18723 | 1.24e-02 | 4.13e-02 | 46 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa049109 | Esophagus | ESCC | Insulin signaling pathway | 89/4205 | 137/8465 | 1.97e-04 | 7.32e-04 | 3.75e-04 | 89 |
| hsa049318 | Esophagus | ESCC | Insulin resistance | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
| hsa0491014 | Esophagus | ESCC | Insulin signaling pathway | 89/4205 | 137/8465 | 1.97e-04 | 7.32e-04 | 3.75e-04 | 89 |
| hsa0493113 | Esophagus | ESCC | Insulin resistance | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
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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 |
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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 |
| PPP1R3D | SNV | Missense_Mutation | c.848N>T | p.Ala283Val | p.A283V | O95685 | protein_coding | tolerated(0.25) | benign(0.085) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PPP1R3D | SNV | Missense_Mutation | c.487N>A | p.Val163Ile | p.V163I | O95685 | protein_coding | tolerated(1) | benign(0) | TCGA-G4-6295-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PPP1R3D | SNV | Missense_Mutation | c.754C>T | p.Arg252Cys | p.R252C | O95685 | protein_coding | tolerated(0.12) | possibly_damaging(0.471) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PPP1R3D | SNV | Missense_Mutation | novel | c.838N>T | p.Arg280Cys | p.R280C | O95685 | protein_coding | deleterious(0) | possibly_damaging(0.642) | TCGA-AX-A2HJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PPP1R3D | SNV | Missense_Mutation | novel | c.434G>A | p.Ser145Asn | p.S145N | O95685 | protein_coding | tolerated(0.2) | benign(0.006) | TCGA-D1-A2G0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PPP1R3D | SNV | Missense_Mutation | rs760835344 | c.641G>A | p.Arg214His | p.R214H | O95685 | protein_coding | tolerated(0.12) | benign(0.06) | TCGA-DF-A2KU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
| PPP1R3D | SNV | Missense_Mutation | c.797A>G | p.Tyr266Cys | p.Y266C | O95685 | protein_coding | deleterious(0) | probably_damaging(0.916) | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD | |
| PPP1R3D | SNV | Missense_Mutation | novel | c.601N>A | p.Glu201Lys | p.E201K | O95685 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-EY-A215-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PPP1R3D | SNV | Missense_Mutation | rs781512014 | c.703G>A | p.Val235Ile | p.V235I | O95685 | protein_coding | tolerated(0.19) | benign(0.015) | TCGA-FI-A2D0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PPP1R3D | SNV | Missense_Mutation | rs768627326 | c.266N>T | p.Pro89Leu | p.P89L | O95685 | protein_coding | tolerated(0.06) | benign(0.003) | TCGA-WQ-AB4B-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
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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 |
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