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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 | RNA-P6T2-P6T2-2 | Human | Lung | IAC | 1.61e-47 | 1.11e+00 | -0.0132 |
166336 | PRICKLE2 | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 2.72e-63 | 1.23e+00 | -0.013 |
166336 | PRICKLE2 | RNA-P6T2-P6T2-4 | Human | Lung | IAC | 9.58e-50 | 1.13e+00 | -0.0121 |
166336 | PRICKLE2 | RNA-P7T1-P7T1-1 | Human | Lung | AIS | 6.92e-13 | 8.47e-01 | -0.0961 |
166336 | PRICKLE2 | RNA-P7T1-P7T1-2 | Human | Lung | AIS | 3.89e-13 | 7.67e-01 | -0.0876 |
166336 | PRICKLE2 | RNA-P7T1-P7T1-3 | Human | Lung | AIS | 5.60e-06 | 5.73e-01 | -0.0822 |
166336 | PRICKLE2 | RNA-P7T1-P7T1-4 | Human | Lung | AIS | 6.36e-10 | 6.38e-01 | -0.0809 |
166336 | PRICKLE2 | RNA-P8T2-P8T2-3 | Human | Lung | AIS | 3.00e-03 | 6.71e-01 | -0.1284 |
166336 | PRICKLE2 | RNA-P8T2-P8T2-4 | Human | Lung | AIS | 6.39e-04 | 8.46e-01 | -0.1197 |
166336 | PRICKLE2 | HTA12-15-2 | Human | Pancreas | PDAC | 3.78e-09 | 5.26e-01 | 0.2315 |
166336 | PRICKLE2 | HTA12-23-1 | Human | Pancreas | PDAC | 8.00e-12 | 8.74e-01 | 0.3405 |
166336 | PRICKLE2 | HTA12-25-1 | Human | Pancreas | PDAC | 3.33e-07 | 5.69e-01 | 0.313 |
166336 | PRICKLE2 | HTA12-26-1 | Human | Pancreas | PDAC | 8.35e-19 | 8.13e-01 | 0.3728 |
166336 | PRICKLE2 | HTA12-29-1 | Human | Pancreas | PDAC | 2.20e-55 | 1.08e+00 | 0.3722 |
166336 | PRICKLE2 | HTA12-30-1 | Human | Pancreas | PDAC | 2.27e-04 | 9.22e-01 | 0.3671 |
166336 | PRICKLE2 | HTA12-32-1 | Human | Pancreas | PDAC | 4.23e-05 | 9.34e-01 | 0.3624 |
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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). |
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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 |
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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. |
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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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