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Gene: PRICKLE2 |
Gene summary for PRICKLE2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PRICKLE2 | Gene ID | 166336 |
| Gene name | prickle planar cell polarity protein 2 | |
| Gene Alias | EPM5 | |
| Cytomap | 3p14.1 | |
| Gene Type | protein-coding | GO ID | GO:0001736 | UniProtAcc | A0A024R368 |
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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 |
| 166336 | PRICKLE2 | TD9 | Human | Lung | IAC | 1.99e-06 | 7.28e-01 | 0.088 |
| 166336 | PRICKLE2 | RNA-P10T2-P10T2-1 | Human | Lung | AAH | 7.31e-03 | 6.35e-01 | -0.1271 |
| 166336 | PRICKLE2 | RNA-P10T2-P10T2-2 | Human | Lung | AAH | 3.17e-04 | 6.62e-01 | -0.1406 |
| 166336 | PRICKLE2 | RNA-P10T2-P10T2-3 | Human | Lung | AAH | 5.95e-04 | 6.21e-01 | -0.1408 |
| 166336 | PRICKLE2 | RNA-P10T2-P10T2-4 | Human | Lung | AAH | 5.54e-03 | 5.57e-01 | -0.138 |
| 166336 | PRICKLE2 | RNA-P17T-P17T-6 | Human | Lung | IAC | 4.71e-02 | 3.31e-01 | 0.3385 |
| 166336 | PRICKLE2 | RNA-P17T-P17T-8 | Human | Lung | IAC | 4.12e-03 | 3.80e-01 | 0.3329 |
| 166336 | PRICKLE2 | RNA-P18T-P18T-2 | Human | Lung | IAC | 2.30e-04 | 9.08e-01 | 0.1129 |
| 166336 | PRICKLE2 | RNA-P18T-P18T-6 | Human | Lung | IAC | 1.73e-02 | 7.53e-01 | 0.0856 |
| 166336 | PRICKLE2 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 1.67e-11 | 4.75e-01 | -0.2116 |
| 166336 | PRICKLE2 | RNA-P25T1-P25T1-2 | Human | Lung | AIS | 2.37e-02 | 4.56e-01 | -0.1941 |
| 166336 | PRICKLE2 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 4.20e-06 | 5.56e-01 | -0.2107 |
| 166336 | PRICKLE2 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 1.40e-11 | 6.77e-01 | -0.2119 |
| 166336 | PRICKLE2 | RNA-P3T-P3T-2 | Human | Lung | IAC | 2.75e-06 | 4.77e-01 | 0.1835 |
| 166336 | PRICKLE2 | RNA-P3T-P3T-4 | Human | Lung | IAC | 5.84e-08 | 5.32e-01 | 0.1859 |
| 166336 | PRICKLE2 | RNA-P6T1-P6T1-1 | Human | Lung | MIAC | 3.36e-06 | 8.88e-01 | -0.0238 |
| 166336 | PRICKLE2 | RNA-P6T1-P6T1-2 | Human | Lung | MIAC | 2.29e-19 | 1.49e+00 | -0.0186 |
| 166336 | PRICKLE2 | RNA-P6T1-P6T1-3 | Human | Lung | MIAC | 2.21e-10 | 1.21e+00 | -0.0296 |
| 166336 | PRICKLE2 | RNA-P6T1-P6T1-4 | Human | Lung | MIAC | 4.04e-15 | 1.24e+00 | -0.0263 |
| 166336 | PRICKLE2 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 2.20e-44 | 1.09e+00 | -0.0166 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma |
| ∗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:00160556 | Lung | IAC | Wnt signaling pathway | 95/2061 | 444/18723 | 1.13e-10 | 2.80e-08 | 95 |
| GO:01987386 | Lung | IAC | cell-cell signaling by wnt | 95/2061 | 446/18723 | 1.46e-10 | 3.48e-08 | 95 |
| GO:00017383 | Lung | IAC | morphogenesis of a polarized epithelium | 21/2061 | 94/18723 | 1.15e-03 | 1.35e-02 | 21 |
| GO:0060071 | Lung | IAC | Wnt signaling pathway, planar cell polarity pathway | 13/2061 | 52/18723 | 3.45e-03 | 2.94e-02 | 13 |
| GO:20000272 | Lung | IAC | regulation of animal organ morphogenesis | 24/2061 | 125/18723 | 4.62e-03 | 3.65e-02 | 24 |
| GO:0090175 | Lung | IAC | regulation of establishment of planar polarity | 13/2061 | 56/18723 | 6.78e-03 | 4.73e-02 | 13 |
| GO:001605512 | Lung | AIS | Wnt signaling pathway | 91/1849 | 444/18723 | 9.38e-12 | 5.47e-09 | 91 |
| GO:019873812 | Lung | AIS | cell-cell signaling by wnt | 91/1849 | 446/18723 | 1.22e-11 | 6.13e-09 | 91 |
| GO:000173811 | Lung | AIS | morphogenesis of a polarized epithelium | 24/1849 | 94/18723 | 1.00e-05 | 4.18e-04 | 24 |
| GO:00600711 | Lung | AIS | Wnt signaling pathway, planar cell polarity pathway | 14/1849 | 52/18723 | 3.82e-04 | 6.66e-03 | 14 |
| GO:0001736 | Lung | AIS | establishment of planar polarity | 17/1849 | 72/18723 | 5.18e-04 | 8.38e-03 | 17 |
| GO:0007164 | Lung | AIS | establishment of tissue polarity | 17/1849 | 72/18723 | 5.18e-04 | 8.38e-03 | 17 |
| GO:00901751 | Lung | AIS | regulation of establishment of planar polarity | 14/1849 | 56/18723 | 8.61e-04 | 1.17e-02 | 14 |
| GO:20000271 | Lung | AIS | regulation of animal organ morphogenesis | 24/1849 | 125/18723 | 1.10e-03 | 1.42e-02 | 24 |
| GO:0035567 | Lung | AIS | non-canonical Wnt signaling pathway | 16/1849 | 72/18723 | 1.50e-03 | 1.81e-02 | 16 |
| GO:001605522 | Lung | AAH | Wnt signaling pathway | 28/613 | 444/18723 | 7.63e-04 | 2.63e-02 | 28 |
| GO:019873822 | Lung | AAH | cell-cell signaling by wnt | 28/613 | 446/18723 | 8.18e-04 | 2.75e-02 | 28 |
| GO:001605531 | Lung | MIAC | Wnt signaling pathway | 50/967 | 444/18723 | 1.88e-07 | 4.02e-05 | 50 |
| GO:019873831 | Lung | MIAC | cell-cell signaling by wnt | 50/967 | 446/18723 | 2.16e-07 | 4.11e-05 | 50 |
| GO:00017382 | Lung | MIAC | morphogenesis of a polarized epithelium | 13/967 | 94/18723 | 1.06e-03 | 2.13e-02 | 13 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa043108 | Lung | IAC | Wnt signaling pathway | 40/1053 | 171/8465 | 4.56e-05 | 7.06e-04 | 4.69e-04 | 40 |
| hsa0431011 | Lung | IAC | Wnt signaling pathway | 40/1053 | 171/8465 | 4.56e-05 | 7.06e-04 | 4.69e-04 | 40 |
| hsa0431021 | Lung | AIS | Wnt signaling pathway | 39/961 | 171/8465 | 1.29e-05 | 3.32e-04 | 2.12e-04 | 39 |
| hsa0431031 | Lung | AIS | Wnt signaling pathway | 39/961 | 171/8465 | 1.29e-05 | 3.32e-04 | 2.12e-04 | 39 |
| hsa0431041 | Lung | MIAC | Wnt signaling pathway | 21/507 | 171/8465 | 1.30e-03 | 1.40e-02 | 1.01e-02 | 21 |
| hsa0431051 | Lung | MIAC | Wnt signaling pathway | 21/507 | 171/8465 | 1.30e-03 | 1.40e-02 | 1.01e-02 | 21 |
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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 |
| PRICKLE2 | SNV | Missense_Mutation | novel | c.1777C>G | p.Leu593Val | p.L593V | protein_coding | deleterious(0.02) | benign(0.108) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD | |
| PRICKLE2 | SNV | Missense_Mutation | rs544405738 | c.1102N>A | p.Asp368Asn | p.D368N | protein_coding | tolerated(0.42) | possibly_damaging(0.734) | TCGA-AO-A0JI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| PRICKLE2 | SNV | Missense_Mutation | novel | c.1502N>T | p.Pro501Leu | p.P501L | protein_coding | tolerated(0.07) | benign(0.023) | TCGA-B6-A0RI-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| PRICKLE2 | SNV | Missense_Mutation | novel | c.1748N>G | p.Val583Gly | p.V583G | protein_coding | tolerated(0.4) | probably_damaging(0.933) | TCGA-BH-A0HX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adrimycin | SD | |
| PRICKLE2 | SNV | Missense_Mutation | novel | c.583N>C | p.Cys195Arg | p.C195R | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-E2-A1IH-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | aromasin | SD | |
| PRICKLE2 | SNV | Missense_Mutation | rs748018197 | c.2308G>A | p.Ala770Thr | p.A770T | protein_coding | tolerated(0.63) | benign(0.121) | TCGA-E9-A5UO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PRICKLE2 | insertion | Nonsense_Mutation | novel | c.1594_1595insTTTCACCGTGTTAGCCGGGATGTTCTCGATCTCCTGACCTCGTGATCC | p.Asp532delinsValSerProCysTerProGlyCysSerArgSerProAspLeuValIleHis | p.D532delinsVSPC*PGCSRSPDLVIH | protein_coding | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| PRICKLE2 | insertion | Frame_Shift_Ins | novel | c.1714_1715insGGGTA | p.Met572ArgfsTer12 | p.M572Rfs*12 | protein_coding | TCGA-AN-A049-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| PRICKLE2 | insertion | Nonsense_Mutation | novel | c.1712_1713insAGAGCTTGAGATGAAATGACATACAAGCTT | p.Ser571_Met572insGluLeuGluMetLysTerHisThrSerPhe | p.S571_M572insELEMK*HTSF | protein_coding | TCGA-AN-A049-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| PRICKLE2 | insertion | Frame_Shift_Ins | novel | c.1499_1500insTCACGCCATTCTCCTGCCTCAG | p.Pro501HisfsTer11 | p.P501Hfs*11 | protein_coding | TCGA-B6-A0RI-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | 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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