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Gene: PKP3 |
Gene summary for PKP3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | PKP3 | Gene ID | 11187 |
Gene name | plakophilin 3 | |
Gene Alias | PKP3 | |
Cytomap | 11p15.5 | |
Gene Type | protein-coding | GO ID | GO:0002159 | UniProtAcc | Q9Y446 |
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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 |
11187 | PKP3 | CA_HPV_1 | Human | Cervix | CC | 9.48e-07 | -1.80e-01 | 0.0264 |
11187 | PKP3 | CA_HPV_3 | Human | Cervix | CC | 1.08e-06 | 3.17e-01 | 0.0414 |
11187 | PKP3 | Tumor | Human | Cervix | CC | 1.15e-34 | 7.61e-01 | 0.1241 |
11187 | PKP3 | sample3 | Human | Cervix | CC | 1.00e-43 | 7.27e-01 | 0.1387 |
11187 | PKP3 | T3 | Human | Cervix | CC | 5.68e-44 | 7.17e-01 | 0.1389 |
11187 | PKP3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.06e-29 | 9.84e-01 | -0.1808 |
11187 | PKP3 | HTA11_2951_2000001011 | Human | Colorectum | AD | 7.74e-03 | 4.11e-01 | 0.0216 |
11187 | PKP3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 8.79e-22 | 8.56e-01 | -0.0811 |
11187 | PKP3 | HTA11_78_2000001011 | Human | Colorectum | AD | 2.42e-10 | 4.64e-01 | -0.1088 |
11187 | PKP3 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.33e-34 | 7.60e-01 | -0.1954 |
11187 | PKP3 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.44e-03 | 1.33e+00 | -0.2602 |
11187 | PKP3 | HTA11_2112_2000001011 | Human | Colorectum | SER | 3.17e-20 | 1.47e+00 | -0.2196 |
11187 | PKP3 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.11e-12 | 7.27e-01 | -0.1207 |
11187 | PKP3 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.76e-12 | 6.95e-01 | -0.1526 |
11187 | PKP3 | HTA11_696_2000001011 | Human | Colorectum | AD | 7.39e-42 | 8.65e-01 | -0.1464 |
11187 | PKP3 | HTA11_866_2000001011 | Human | Colorectum | AD | 7.39e-24 | 5.57e-01 | -0.1001 |
11187 | PKP3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.78e-28 | 9.32e-01 | -0.059 |
11187 | PKP3 | HTA11_2992_2000001011 | Human | Colorectum | SER | 3.65e-13 | 9.94e-01 | -0.1706 |
11187 | PKP3 | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.31e-05 | 4.98e-01 | -0.2061 |
11187 | PKP3 | HTA11_5216_2000001011 | Human | Colorectum | SER | 9.50e-09 | 8.62e-01 | -0.1462 |
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Transcriptomic changes along malignancy continuum. |
∗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:007265910 | Cervix | CC | protein localization to plasma membrane | 73/2311 | 284/18723 | 4.95e-10 | 6.73e-08 | 73 |
GO:19907788 | Cervix | CC | protein localization to cell periphery | 78/2311 | 333/18723 | 1.22e-08 | 9.73e-07 | 78 |
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:00029347 | Cervix | CC | desmosome organization | 7/2311 | 10/18723 | 3.69e-05 | 5.84e-04 | 7 |
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: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 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
PKP3 | deletion | Frame_Shift_Del | novel | c.1261delN | p.Asn422MetfsTer15 | p.N422Mfs*15 | Q9Y446 | protein_coding | TCGA-BR-6802-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Ancillary | leucovorin | CR | ||
PKP3 | deletion | Frame_Shift_Del | rs751960573 | c.1378delN | p.Gly461ValfsTer186 | p.G461Vfs*186 | Q9Y446 | protein_coding | TCGA-CD-A4MG-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | ||
PKP3 | insertion | Frame_Shift_Ins | rs781609202 | c.1383_1384insC | p.Leu464ProfsTer224 | p.L464Pfs*224 | Q9Y446 | protein_coding | TCGA-HF-A5NB-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | fluorouracil | 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 |
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