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Gene: PKP1 |
Gene summary for PKP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PKP1 | Gene ID | 5317 |
| Gene name | plakophilin 1 | |
| Gene Alias | B6P | |
| Cytomap | 1q32.1 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q13835 |
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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 |
| 5317 | PKP1 | CA_HPV_1 | Human | Cervix | CC | 3.82e-10 | -3.23e-01 | 0.0264 |
| 5317 | PKP1 | CA_HPV_3 | Human | Cervix | CC | 4.59e-11 | 4.19e-01 | 0.0414 |
| 5317 | PKP1 | HSIL_HPV_1 | Human | Cervix | HSIL_HPV | 7.11e-04 | -3.17e-01 | 0.0116 |
| 5317 | PKP1 | HSIL_HPV_2 | Human | Cervix | HSIL_HPV | 2.44e-03 | -2.77e-01 | 0.0208 |
| 5317 | PKP1 | N_HPV_2 | Human | Cervix | N_HPV | 5.12e-06 | 3.95e-01 | -0.0131 |
| 5317 | PKP1 | CCI_1 | Human | Cervix | CC | 1.36e-11 | 1.08e+00 | 0.528 |
| 5317 | PKP1 | CCI_3 | Human | Cervix | CC | 2.38e-10 | 1.05e+00 | 0.516 |
| 5317 | PKP1 | Tumor | Human | Cervix | CC | 4.39e-32 | 7.30e-01 | 0.1241 |
| 5317 | PKP1 | sample3 | Human | Cervix | CC | 4.47e-38 | 6.63e-01 | 0.1387 |
| 5317 | PKP1 | T3 | Human | Cervix | CC | 2.01e-37 | 6.86e-01 | 0.1389 |
| 5317 | PKP1 | LZE2T | Human | Esophagus | ESCC | 9.78e-07 | 1.68e+00 | 0.082 |
| 5317 | PKP1 | LZE4T | Human | Esophagus | ESCC | 3.00e-22 | 9.42e-01 | 0.0811 |
| 5317 | PKP1 | LZE5T | Human | Esophagus | ESCC | 2.34e-02 | -1.12e-01 | 0.0514 |
| 5317 | PKP1 | LZE7T | Human | Esophagus | ESCC | 1.55e-13 | 1.38e+00 | 0.0667 |
| 5317 | PKP1 | LZE8T | Human | Esophagus | ESCC | 1.75e-08 | 4.25e-01 | 0.067 |
| 5317 | PKP1 | LZE20T | Human | Esophagus | ESCC | 1.10e-06 | 2.21e-01 | 0.0662 |
| 5317 | PKP1 | LZE21D1 | Human | Esophagus | HGIN | 5.70e-03 | 8.88e-01 | 0.0632 |
| 5317 | PKP1 | LZE22D1 | Human | Esophagus | HGIN | 7.87e-05 | 2.17e-02 | 0.0595 |
| 5317 | PKP1 | LZE22T | Human | Esophagus | ESCC | 7.16e-03 | 7.79e-01 | 0.068 |
| 5317 | PKP1 | LZE24T | Human | Esophagus | ESCC | 2.48e-08 | 7.42e-01 | 0.0596 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| 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:00452169 | Cervix | CC | cell-cell junction organization | 53/2311 | 200/18723 | 3.83e-08 | 2.53e-06 | 53 |
| GO:003133010 | Cervix | CC | negative regulation of cellular catabolic process | 63/2311 | 262/18723 | 1.10e-07 | 5.68e-06 | 63 |
| GO:00343298 | Cervix | CC | cell junction assembly | 88/2311 | 420/18723 | 3.42e-07 | 1.38e-05 | 88 |
| GO:00064029 | Cervix | CC | mRNA catabolic process | 56/2311 | 232/18723 | 4.81e-07 | 1.83e-05 | 56 |
| GO:19033119 | Cervix | CC | regulation of mRNA metabolic process | 64/2311 | 288/18723 | 1.71e-06 | 5.64e-05 | 64 |
| GO:00070439 | Cervix | CC | cell-cell junction assembly | 39/2311 | 146/18723 | 1.86e-06 | 5.94e-05 | 39 |
| GO:000989510 | Cervix | CC | negative regulation of catabolic process | 69/2311 | 320/18723 | 2.15e-06 | 6.55e-05 | 69 |
| GO:00064019 | Cervix | CC | RNA catabolic process | 62/2311 | 278/18723 | 2.18e-06 | 6.56e-05 | 62 |
| GO:00610139 | Cervix | CC | regulation of mRNA catabolic process | 38/2311 | 166/18723 | 1.07e-04 | 1.36e-03 | 38 |
| GO:190331210 | Cervix | CC | negative regulation of mRNA metabolic process | 24/2311 | 92/18723 | 2.49e-04 | 2.77e-03 | 24 |
| GO:00467008 | Cervix | CC | heterocycle catabolic process | 80/2311 | 445/18723 | 3.23e-04 | 3.42e-03 | 80 |
| GO:00346559 | Cervix | CC | nucleobase-containing compound catabolic process | 74/2311 | 407/18723 | 3.77e-04 | 3.88e-03 | 74 |
| GO:00442709 | Cervix | CC | cellular nitrogen compound catabolic process | 79/2311 | 451/18723 | 7.80e-04 | 6.91e-03 | 79 |
| GO:00451043 | Cervix | CC | intermediate filament cytoskeleton organization | 15/2311 | 51/18723 | 9.25e-04 | 7.84e-03 | 15 |
| GO:00451033 | Cervix | CC | intermediate filament-based process | 15/2311 | 52/18723 | 1.15e-03 | 9.39e-03 | 15 |
| GO:19023698 | Cervix | CC | negative regulation of RNA catabolic process | 19/2311 | 75/18723 | 1.54e-03 | 1.19e-02 | 19 |
| GO:00194398 | Cervix | CC | aromatic compound catabolic process | 79/2311 | 467/18723 | 2.14e-03 | 1.54e-02 | 79 |
| GO:19013618 | Cervix | CC | organic cyclic compound catabolic process | 80/2311 | 495/18723 | 6.77e-03 | 3.72e-02 | 80 |
| GO:19023738 | Cervix | CC | negative regulation of mRNA catabolic process | 15/2311 | 63/18723 | 8.52e-03 | 4.40e-02 | 15 |
| GO:004521614 | Cervix | HSIL_HPV | cell-cell junction organization | 23/737 | 200/18723 | 4.21e-06 | 1.69e-04 | 23 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 |
| PKP1 | SNV | Missense_Mutation | c.1309N>A | p.Ala437Thr | p.A437T | Q13835 | protein_coding | deleterious(0.01) | possibly_damaging(0.505) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PKP1 | SNV | Missense_Mutation | c.1600N>C | p.Glu534Gln | p.E534Q | Q13835 | protein_coding | tolerated(0.18) | benign(0.424) | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | |
| PKP1 | SNV | Missense_Mutation | c.1738N>T | p.Gly580Trp | p.G580W | Q13835 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A0E9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR | |
| PKP1 | SNV | Missense_Mutation | c.547N>T | p.Arg183Cys | p.R183C | Q13835 | protein_coding | deleterious(0) | benign(0.306) | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PKP1 | SNV | Missense_Mutation | rs781340038 | c.548N>A | p.Arg183His | p.R183H | Q13835 | protein_coding | deleterious(0.03) | benign(0) | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PKP1 | SNV | Missense_Mutation | rs751817941 | c.1454G>A | p.Arg485His | p.R485H | Q13835 | protein_coding | tolerated(0.06) | benign(0.067) | TCGA-E9-A1NC-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| PKP1 | insertion | In_Frame_Ins | novel | c.1880_1881insAGGGGAAATGAGACTTCCCTCTCTCCACCCATCTGG | p.Leu627_Leu628insGlyGluMetArgLeuProSerLeuHisProSerGly | p.L627_L628insGEMRLPSLHPSG | Q13835 | protein_coding | TCGA-AN-A0FK-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| PKP1 | deletion | Frame_Shift_Del | novel | c.1740delG | p.Leu581Ter | p.L581* | Q13835 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| PKP1 | deletion | Frame_Shift_Del | novel | c.2172delA | p.Gly725ValfsTer10 | p.G725Vfs*10 | Q13835 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| PKP1 | SNV | Missense_Mutation | novel | c.97A>G | p.Thr33Ala | p.T33A | Q13835 | protein_coding | tolerated(0.12) | benign(0.437) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 |
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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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