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Gene: PLEKHA4 |
Gene summary for PLEKHA4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PLEKHA4 | Gene ID | 57664 |
| Gene name | pleckstrin homology domain containing A4 | |
| Gene Alias | PEPP1 | |
| Cytomap | 19q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0001736 | UniProtAcc | Q9H4M7 |
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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 |
| 57664 | PLEKHA4 | C43 | Human | Oral cavity | OSCC | 1.05e-09 | 2.01e-01 | 0.1704 |
| 57664 | PLEKHA4 | C46 | Human | Oral cavity | OSCC | 2.70e-07 | 3.24e-01 | 0.1673 |
| 57664 | PLEKHA4 | C08 | Human | Oral cavity | OSCC | 6.13e-13 | 3.10e-01 | 0.1919 |
| 57664 | PLEKHA4 | LN46 | Human | Oral cavity | OSCC | 4.75e-06 | 5.17e-01 | 0.1666 |
| 57664 | PLEKHA4 | NEOLP-1 | Human | Oral cavity | NEOLP | 1.19e-02 | 1.73e-01 | -0.0194 |
| 57664 | PLEKHA4 | NEOLP-3 | Human | Oral cavity | NEOLP | 4.41e-09 | 3.37e-01 | -0.0191 |
| 57664 | PLEKHA4 | SYSMH2 | Human | Oral cavity | OSCC | 6.07e-20 | 4.83e-01 | 0.2326 |
| 57664 | PLEKHA4 | SYSMH3 | Human | Oral cavity | OSCC | 3.56e-20 | 4.28e-01 | 0.2442 |
| 57664 | PLEKHA4 | SYSMH4 | Human | Oral cavity | OSCC | 2.48e-06 | 1.88e-01 | 0.1226 |
| 57664 | PLEKHA4 | male-WTA | Human | Thyroid | PTC | 1.91e-31 | 4.02e-01 | 0.1037 |
| 57664 | PLEKHA4 | PTC01 | Human | Thyroid | PTC | 3.79e-28 | 5.61e-01 | 0.1899 |
| 57664 | PLEKHA4 | PTC03 | Human | Thyroid | PTC | 2.43e-05 | 3.29e-01 | 0.1784 |
| 57664 | PLEKHA4 | PTC04 | Human | Thyroid | PTC | 6.02e-09 | 2.86e-01 | 0.1927 |
| 57664 | PLEKHA4 | PTC05 | Human | Thyroid | PTC | 2.87e-31 | 9.99e-01 | 0.2065 |
| 57664 | PLEKHA4 | PTC06 | Human | Thyroid | PTC | 6.16e-43 | 8.99e-01 | 0.2057 |
| 57664 | PLEKHA4 | PTC07 | Human | Thyroid | PTC | 7.49e-47 | 7.15e-01 | 0.2044 |
| 57664 | PLEKHA4 | ATC09 | Human | Thyroid | ATC | 2.35e-02 | 1.13e-01 | 0.2871 |
| 57664 | PLEKHA4 | ATC12 | Human | Thyroid | ATC | 6.20e-08 | 2.26e-01 | 0.34 |
| 57664 | PLEKHA4 | ATC13 | Human | Thyroid | ATC | 1.00e-11 | 1.13e-01 | 0.34 |
| 57664 | PLEKHA4 | ATC1 | Human | Thyroid | ATC | 6.40e-03 | 1.40e-01 | 0.2878 |
| Page: 1 2 3 4 5 |
| 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 | ||
| 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:001605517 | Esophagus | ESCC | Wnt signaling pathway | 268/8552 | 444/18723 | 2.32e-10 | 6.58e-09 | 268 |
| GO:019873817 | Esophagus | ESCC | cell-cell signaling by wnt | 269/8552 | 446/18723 | 2.41e-10 | 6.79e-09 | 269 |
| GO:003011117 | Esophagus | ESCC | regulation of Wnt signaling pathway | 194/8552 | 328/18723 | 5.39e-07 | 7.14e-06 | 194 |
| GO:006007016 | Esophagus | ESCC | canonical Wnt signaling pathway | 180/8552 | 303/18723 | 9.15e-07 | 1.17e-05 | 180 |
| GO:006082817 | Esophagus | ESCC | regulation of canonical Wnt signaling pathway | 153/8552 | 253/18723 | 1.38e-06 | 1.67e-05 | 153 |
| GO:00017387 | Esophagus | ESCC | morphogenesis of a polarized epithelium | 63/8552 | 94/18723 | 2.34e-05 | 2.00e-04 | 63 |
| GO:009026316 | Esophagus | ESCC | positive regulation of canonical Wnt signaling pathway | 69/8552 | 106/18723 | 4.22e-05 | 3.39e-04 | 69 |
| GO:003017716 | Esophagus | ESCC | positive regulation of Wnt signaling pathway | 87/8552 | 140/18723 | 6.18e-05 | 4.73e-04 | 87 |
| GO:00600714 | Esophagus | ESCC | Wnt signaling pathway, planar cell polarity pathway | 36/8552 | 52/18723 | 5.05e-04 | 2.79e-03 | 36 |
| GO:00901753 | Esophagus | ESCC | regulation of establishment of planar polarity | 37/8552 | 56/18723 | 1.65e-03 | 7.65e-03 | 37 |
| GO:00017361 | Esophagus | ESCC | establishment of planar polarity | 45/8552 | 72/18723 | 2.97e-03 | 1.24e-02 | 45 |
| GO:00071641 | Esophagus | ESCC | establishment of tissue polarity | 45/8552 | 72/18723 | 2.97e-03 | 1.24e-02 | 45 |
| GO:00355671 | Esophagus | ESCC | non-canonical Wnt signaling pathway | 45/8552 | 72/18723 | 2.97e-03 | 1.24e-02 | 45 |
| GO:20000274 | Esophagus | ESCC | regulation of animal organ morphogenesis | 71/8552 | 125/18723 | 7.97e-03 | 2.84e-02 | 71 |
| GO:001605511 | Liver | Cirrhotic | Wnt signaling pathway | 150/4634 | 444/18723 | 9.75e-06 | 1.42e-04 | 150 |
| GO:019873811 | Liver | Cirrhotic | cell-cell signaling by wnt | 150/4634 | 446/18723 | 1.28e-05 | 1.80e-04 | 150 |
| GO:003011111 | Liver | Cirrhotic | regulation of Wnt signaling pathway | 112/4634 | 328/18723 | 7.57e-05 | 8.40e-04 | 112 |
| GO:006082811 | Liver | Cirrhotic | regulation of canonical Wnt signaling pathway | 86/4634 | 253/18723 | 5.70e-04 | 4.46e-03 | 86 |
| GO:009026311 | Liver | Cirrhotic | positive regulation of canonical Wnt signaling pathway | 41/4634 | 106/18723 | 1.02e-03 | 7.16e-03 | 41 |
| GO:006007011 | Liver | Cirrhotic | canonical Wnt signaling pathway | 97/4634 | 303/18723 | 2.42e-03 | 1.46e-02 | 97 |
| Page: 1 2 3 4 |
| 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 |
| PLEKHA4 | SNV | Missense_Mutation | rs369327643 | c.344N>A | p.Arg115Gln | p.R115Q | Q9H4M7 | protein_coding | tolerated(0.32) | probably_damaging(0.971) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| PLEKHA4 | SNV | Missense_Mutation | novel | c.2088N>T | p.Leu696Phe | p.L696F | Q9H4M7 | protein_coding | deleterious_low_confidence(0.02) | possibly_damaging(0.69) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PLEKHA4 | SNV | Missense_Mutation | rs763707559 | c.1678N>T | p.Pro560Ser | p.P560S | Q9H4M7 | protein_coding | deleterious(0.01) | benign(0.276) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PLEKHA4 | SNV | Missense_Mutation | c.1456N>G | p.Met486Val | p.M486V | Q9H4M7 | protein_coding | deleterious(0.03) | benign(0.138) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PLEKHA4 | SNV | Missense_Mutation | c.577N>C | p.Glu193Gln | p.E193Q | Q9H4M7 | protein_coding | deleterious(0.01) | probably_damaging(0.986) | TCGA-C8-A12P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PLEKHA4 | SNV | Missense_Mutation | novel | c.584N>T | p.Pro195Leu | p.P195L | Q9H4M7 | protein_coding | deleterious(0.04) | possibly_damaging(0.46) | TCGA-C8-A8HQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PLEKHA4 | insertion | Frame_Shift_Ins | novel | c.855_856insTGTTTTGCCAGGCTGGTGCATTTATTATCACCCTCTGTGT | p.Pro286CysfsTer32 | p.P286Cfs*32 | Q9H4M7 | protein_coding | TCGA-A8-A08X-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | PD | ||
| PLEKHA4 | SNV | Missense_Mutation | c.461N>T | p.Ala154Val | p.A154V | Q9H4M7 | protein_coding | tolerated(0.42) | possibly_damaging(0.452) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PLEKHA4 | SNV | Missense_Mutation | c.1999N>A | p.Glu667Lys | p.E667K | Q9H4M7 | protein_coding | deleterious_low_confidence(0.04) | benign(0.027) | TCGA-LP-A4AV-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PLEKHA4 | SNV | Missense_Mutation | c.2132C>T | p.Ser711Leu | p.S711L | Q9H4M7 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.953) | TCGA-ZJ-AAXD-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | 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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