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Gene: PRKD3 |
Gene summary for PRKD3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PRKD3 | Gene ID | 23683 |
| Gene name | protein kinase D3 | |
| Gene Alias | EPK2 | |
| Cytomap | 2p22.2 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | O94806 |
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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 |
| 23683 | PRKD3 | LZE4T | Human | Esophagus | ESCC | 1.04e-05 | 7.28e-02 | 0.0811 |
| 23683 | PRKD3 | LZE5T | Human | Esophagus | ESCC | 1.33e-05 | 2.29e-01 | 0.0514 |
| 23683 | PRKD3 | LZE7T | Human | Esophagus | ESCC | 8.57e-03 | 2.88e-01 | 0.0667 |
| 23683 | PRKD3 | LZE24T | Human | Esophagus | ESCC | 1.28e-06 | 1.12e-01 | 0.0596 |
| 23683 | PRKD3 | LZE6T | Human | Esophagus | ESCC | 2.18e-02 | 1.09e-01 | 0.0845 |
| 23683 | PRKD3 | P1T-E | Human | Esophagus | ESCC | 2.96e-03 | 1.43e-01 | 0.0875 |
| 23683 | PRKD3 | P2T-E | Human | Esophagus | ESCC | 2.60e-24 | 5.27e-01 | 0.1177 |
| 23683 | PRKD3 | P4T-E | Human | Esophagus | ESCC | 5.54e-06 | 1.30e-01 | 0.1323 |
| 23683 | PRKD3 | P5T-E | Human | Esophagus | ESCC | 8.69e-03 | -2.99e-02 | 0.1327 |
| 23683 | PRKD3 | P8T-E | Human | Esophagus | ESCC | 3.15e-11 | 1.06e-01 | 0.0889 |
| 23683 | PRKD3 | P9T-E | Human | Esophagus | ESCC | 9.14e-09 | 8.33e-02 | 0.1131 |
| 23683 | PRKD3 | P10T-E | Human | Esophagus | ESCC | 6.36e-14 | 9.84e-02 | 0.116 |
| 23683 | PRKD3 | P11T-E | Human | Esophagus | ESCC | 1.02e-13 | 4.83e-01 | 0.1426 |
| 23683 | PRKD3 | P12T-E | Human | Esophagus | ESCC | 8.94e-06 | 1.25e-01 | 0.1122 |
| 23683 | PRKD3 | P15T-E | Human | Esophagus | ESCC | 9.42e-10 | 1.79e-01 | 0.1149 |
| 23683 | PRKD3 | P16T-E | Human | Esophagus | ESCC | 2.82e-27 | 4.52e-01 | 0.1153 |
| 23683 | PRKD3 | P17T-E | Human | Esophagus | ESCC | 3.26e-06 | 1.75e-01 | 0.1278 |
| 23683 | PRKD3 | P19T-E | Human | Esophagus | ESCC | 2.10e-04 | 2.03e-01 | 0.1662 |
| 23683 | PRKD3 | P20T-E | Human | Esophagus | ESCC | 3.29e-06 | 1.47e-01 | 0.1124 |
| 23683 | PRKD3 | P21T-E | Human | Esophagus | ESCC | 6.58e-07 | 9.65e-02 | 0.1617 |
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| 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 | ||
| 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:00066433 | Esophagus | ESCC | membrane lipid metabolic process | 130/8552 | 203/18723 | 9.29e-08 | 1.54e-06 | 130 |
| GO:00464673 | Esophagus | ESCC | membrane lipid biosynthetic process | 91/8552 | 142/18723 | 7.19e-06 | 7.19e-05 | 91 |
| GO:00066652 | Esophagus | ESCC | sphingolipid metabolic process | 96/8552 | 155/18723 | 3.21e-05 | 2.66e-04 | 96 |
| GO:00301481 | Esophagus | ESCC | sphingolipid biosynthetic process | 62/8552 | 103/18723 | 2.10e-03 | 9.38e-03 | 62 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05208211 | Esophagus | ESCC | Chemical carcinogenesis - reactive oxygen species | 168/4205 | 223/8465 | 1.83e-15 | 6.81e-14 | 3.49e-14 | 168 |
| hsa05208310 | Esophagus | ESCC | Chemical carcinogenesis - reactive oxygen species | 168/4205 | 223/8465 | 1.83e-15 | 6.81e-14 | 3.49e-14 | 168 |
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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 |
| PRKD3 | SNV | Missense_Mutation | c.715N>C | p.Glu239Gln | p.E239Q | O94806 | protein_coding | tolerated(0.28) | benign(0.063) | TCGA-A2-A0YK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| PRKD3 | SNV | Missense_Mutation | c.19N>G | p.Pro7Ala | p.P7A | O94806 | protein_coding | deleterious_low_confidence(0) | benign(0.046) | TCGA-A8-A081-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PRKD3 | SNV | Missense_Mutation | c.594N>G | p.Phe198Leu | p.F198L | O94806 | protein_coding | tolerated(0.08) | benign(0.225) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PRKD3 | SNV | Missense_Mutation | c.1582N>T | p.Arg528Cys | p.R528C | O94806 | protein_coding | deleterious(0.02) | probably_damaging(0.975) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PRKD3 | SNV | Missense_Mutation | c.1738N>C | p.Glu580Gln | p.E580Q | O94806 | protein_coding | deleterious(0) | possibly_damaging(0.903) | TCGA-AO-A0JC-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | SD | |
| PRKD3 | SNV | Missense_Mutation | c.2284N>A | p.Val762Met | p.V762M | O94806 | protein_coding | deleterious(0.02) | probably_damaging(0.994) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| PRKD3 | insertion | Nonsense_Mutation | novel | c.158_159insTTTAGATCTTGTTTAGGAAGATTCTGAA | p.Arg54LeufsTer5 | p.R54Lfs*5 | O94806 | protein_coding | TCGA-A8-A0A6-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | epirubicin | CR | ||
| PRKD3 | SNV | Missense_Mutation | novel | c.2537C>T | p.Thr846Ile | p.T846I | O94806 | protein_coding | tolerated(0.2) | benign(0.129) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PRKD3 | SNV | Missense_Mutation | novel | c.2242C>T | p.Leu748Phe | p.L748F | O94806 | protein_coding | deleterious(0.02) | possibly_damaging(0.739) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PRKD3 | SNV | Missense_Mutation | c.1879N>A | p.Leu627Ile | p.L627I | O94806 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | 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 |
| 23683 | PRKD3 | KINASE, ENZYME, SERINE THREONINE KINASE, DRUGGABLE GENOME | CENISERTIB | CENISERTIB | ||
| 23683 | PRKD3 | KINASE, ENZYME, SERINE THREONINE KINASE, DRUGGABLE GENOME | inhibitor | CHEMBL565612 | SOTRASTAURIN | |
| 23683 | PRKD3 | KINASE, ENZYME, SERINE THREONINE KINASE, DRUGGABLE GENOME | BRYOSTATIN-1 | |||
| 23683 | PRKD3 | KINASE, ENZYME, SERINE THREONINE KINASE, DRUGGABLE GENOME | GEFITINIB | GEFITINIB | ||
| 23683 | PRKD3 | KINASE, ENZYME, SERINE THREONINE KINASE, DRUGGABLE GENOME | BMS-387032 | BMS-387032 | ||
| 23683 | PRKD3 | KINASE, ENZYME, SERINE THREONINE KINASE, DRUGGABLE GENOME | inhibitor | 249565728 | ||
| 23683 | PRKD3 | KINASE, ENZYME, SERINE THREONINE KINASE, DRUGGABLE GENOME | GW441756X | GW441756X | ||
| 23683 | PRKD3 | KINASE, ENZYME, SERINE THREONINE KINASE, DRUGGABLE GENOME | BAY-613606 | CHEMBL541400 | ||
| 23683 | PRKD3 | KINASE, ENZYME, SERINE THREONINE KINASE, DRUGGABLE GENOME | R-1487 | R-1487 | ||
| 23683 | PRKD3 | KINASE, ENZYME, SERINE THREONINE KINASE, DRUGGABLE GENOME | JNJ-7706621 | JNJ-7706621 |
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