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Gene: PRKDC |
Gene summary for PRKDC |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PRKDC | Gene ID | 5591 |
| Gene name | protein kinase, DNA-activated, catalytic subunit | |
| Gene Alias | DNA-PKC | |
| Cytomap | 8q11.21 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P78527 |
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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 |
| 5591 | PRKDC | GSM4909281 | Human | Breast | IDC | 9.06e-13 | 3.90e-01 | 0.21 |
| 5591 | PRKDC | GSM4909282 | Human | Breast | IDC | 9.19e-13 | 3.20e-01 | -0.0288 |
| 5591 | PRKDC | GSM4909285 | Human | Breast | IDC | 2.06e-08 | 2.47e-01 | 0.21 |
| 5591 | PRKDC | GSM4909287 | Human | Breast | IDC | 5.12e-06 | 3.20e-01 | 0.2057 |
| 5591 | PRKDC | GSM4909291 | Human | Breast | IDC | 6.44e-05 | 3.39e-01 | 0.1753 |
| 5591 | PRKDC | GSM4909293 | Human | Breast | IDC | 1.36e-51 | 7.30e-01 | 0.1581 |
| 5591 | PRKDC | GSM4909301 | Human | Breast | IDC | 1.79e-06 | 2.61e-01 | 0.1577 |
| 5591 | PRKDC | GSM4909304 | Human | Breast | IDC | 1.33e-30 | 5.56e-01 | 0.1636 |
| 5591 | PRKDC | GSM4909306 | Human | Breast | IDC | 3.46e-09 | 3.13e-01 | 0.1564 |
| 5591 | PRKDC | GSM4909307 | Human | Breast | IDC | 3.54e-02 | 1.48e-01 | 0.1569 |
| 5591 | PRKDC | GSM4909311 | Human | Breast | IDC | 1.44e-05 | -5.70e-02 | 0.1534 |
| 5591 | PRKDC | GSM4909317 | Human | Breast | IDC | 2.66e-24 | 6.06e-01 | 0.1355 |
| 5591 | PRKDC | GSM4909319 | Human | Breast | IDC | 1.92e-08 | -6.15e-02 | 0.1563 |
| 5591 | PRKDC | GSM4909321 | Human | Breast | IDC | 4.89e-02 | 1.72e-03 | 0.1559 |
| 5591 | PRKDC | brca2 | Human | Breast | Precancer | 6.07e-07 | 9.07e-02 | -0.024 |
| 5591 | PRKDC | M1 | Human | Breast | IDC | 9.38e-12 | 4.79e-01 | 0.1577 |
| 5591 | PRKDC | NCCBC2 | Human | Breast | DCIS | 2.32e-05 | 4.21e-01 | 0.1554 |
| 5591 | PRKDC | NCCBC3 | Human | Breast | DCIS | 3.68e-09 | 3.35e-01 | 0.1198 |
| 5591 | PRKDC | P1 | Human | Breast | IDC | 9.14e-05 | 6.90e-02 | 0.1527 |
| 5591 | PRKDC | P2 | Human | Breast | IDC | 4.83e-09 | 4.94e-01 | 0.21 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:00226139 | Breast | Precancer | ribonucleoprotein complex biogenesis | 79/1080 | 463/18723 | 2.11e-18 | 1.03e-15 | 79 |
| GO:00971939 | Breast | Precancer | intrinsic apoptotic signaling pathway | 59/1080 | 288/18723 | 8.07e-18 | 3.60e-15 | 59 |
| GO:00718269 | Breast | Precancer | ribonucleoprotein complex subunit organization | 48/1080 | 227/18723 | 2.68e-15 | 8.45e-13 | 48 |
| GO:00226189 | Breast | Precancer | ribonucleoprotein complex assembly | 47/1080 | 220/18723 | 3.47e-15 | 1.03e-12 | 47 |
| GO:00422549 | Breast | Precancer | ribosome biogenesis | 52/1080 | 299/18723 | 7.35e-13 | 1.51e-10 | 52 |
| GO:00064179 | Breast | Precancer | regulation of translation | 67/1080 | 468/18723 | 4.71e-12 | 7.64e-10 | 67 |
| GO:00457279 | Breast | Precancer | positive regulation of translation | 32/1080 | 136/18723 | 5.89e-12 | 9.27e-10 | 32 |
| GO:00422559 | Breast | Precancer | ribosome assembly | 21/1080 | 61/18723 | 1.06e-11 | 1.53e-09 | 21 |
| GO:00342509 | Breast | Precancer | positive regulation of cellular amide metabolic process | 33/1080 | 162/18723 | 1.72e-10 | 1.77e-08 | 33 |
| GO:00422749 | Breast | Precancer | ribosomal small subunit biogenesis | 21/1080 | 73/18723 | 4.84e-10 | 4.39e-08 | 21 |
| GO:00000289 | Breast | Precancer | ribosomal small subunit assembly | 10/1080 | 19/18723 | 2.24e-08 | 1.50e-06 | 10 |
| GO:00063646 | Breast | Precancer | rRNA processing | 35/1080 | 225/18723 | 7.90e-08 | 4.60e-06 | 35 |
| GO:00160726 | Breast | Precancer | rRNA metabolic process | 36/1080 | 236/18723 | 8.59e-08 | 4.84e-06 | 36 |
| GO:00022629 | Breast | Precancer | myeloid cell homeostasis | 27/1080 | 157/18723 | 3.10e-07 | 1.49e-05 | 27 |
| GO:00341019 | Breast | Precancer | erythrocyte homeostasis | 23/1080 | 129/18723 | 1.20e-06 | 4.60e-05 | 23 |
| GO:00316479 | Breast | Precancer | regulation of protein stability | 38/1080 | 298/18723 | 3.73e-06 | 1.19e-04 | 38 |
| GO:00300999 | Breast | Precancer | myeloid cell differentiation | 45/1080 | 381/18723 | 4.00e-06 | 1.25e-04 | 45 |
| GO:00075688 | Breast | Precancer | aging | 41/1080 | 339/18723 | 5.95e-06 | 1.71e-04 | 41 |
| GO:00487329 | Breast | Precancer | gland development | 49/1080 | 436/18723 | 6.11e-06 | 1.73e-04 | 49 |
| GO:00103323 | Breast | Precancer | response to gamma radiation | 13/1080 | 56/18723 | 1.35e-05 | 3.38e-04 | 13 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa041106 | Cervix | CC | Cell cycle | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
| hsa0411013 | Cervix | CC | Cell cycle | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
| hsa041109 | Esophagus | HGIN | Cell cycle | 38/1383 | 157/8465 | 6.70e-03 | 4.37e-02 | 3.47e-02 | 38 |
| hsa0411016 | Esophagus | HGIN | Cell cycle | 38/1383 | 157/8465 | 6.70e-03 | 4.37e-02 | 3.47e-02 | 38 |
| hsa0411023 | Esophagus | ESCC | Cell cycle | 126/4205 | 157/8465 | 1.34e-15 | 5.60e-14 | 2.87e-14 | 126 |
| hsa0411033 | Esophagus | ESCC | Cell cycle | 126/4205 | 157/8465 | 1.34e-15 | 5.60e-14 | 2.87e-14 | 126 |
| hsa041104 | Liver | Cirrhotic | Cell cycle | 61/2530 | 157/8465 | 9.53e-03 | 3.21e-02 | 1.98e-02 | 61 |
| hsa0411011 | Liver | Cirrhotic | Cell cycle | 61/2530 | 157/8465 | 9.53e-03 | 3.21e-02 | 1.98e-02 | 61 |
| hsa041102 | Liver | HCC | Cell cycle | 106/4020 | 157/8465 | 2.54e-07 | 3.04e-06 | 1.69e-06 | 106 |
| hsa041103 | Liver | HCC | Cell cycle | 106/4020 | 157/8465 | 2.54e-07 | 3.04e-06 | 1.69e-06 | 106 |
| hsa041105 | Lung | IAC | Cell cycle | 30/1053 | 157/8465 | 1.03e-02 | 3.83e-02 | 2.54e-02 | 30 |
| hsa0411012 | Lung | IAC | Cell cycle | 30/1053 | 157/8465 | 1.03e-02 | 3.83e-02 | 2.54e-02 | 30 |
| hsa041108 | Oral cavity | OSCC | Cell cycle | 118/3704 | 157/8465 | 7.15e-16 | 2.66e-14 | 1.35e-14 | 118 |
| hsa0411015 | Oral cavity | OSCC | Cell cycle | 118/3704 | 157/8465 | 7.15e-16 | 2.66e-14 | 1.35e-14 | 118 |
| hsa0411022 | Oral cavity | LP | Cell cycle | 70/2418 | 157/8465 | 1.17e-05 | 8.27e-05 | 5.33e-05 | 70 |
| hsa0411032 | Oral cavity | LP | Cell cycle | 70/2418 | 157/8465 | 1.17e-05 | 8.27e-05 | 5.33e-05 | 70 |
| hsa0411041 | Oral cavity | EOLP | Cell cycle | 42/1218 | 157/8465 | 3.20e-05 | 1.61e-04 | 9.52e-05 | 42 |
| hsa0411051 | Oral cavity | EOLP | Cell cycle | 42/1218 | 157/8465 | 3.20e-05 | 1.61e-04 | 9.52e-05 | 42 |
| hsa0411061 | Oral cavity | NEOLP | Cell cycle | 37/1112 | 157/8465 | 2.29e-04 | 1.58e-03 | 9.95e-04 | 37 |
| hsa0411071 | Oral cavity | NEOLP | Cell cycle | 37/1112 | 157/8465 | 2.29e-04 | 1.58e-03 | 9.95e-04 | 37 |
| Page: 1 2 |
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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 |
| PRKDC | SNV | Missense_Mutation | c.1855G>C | p.Asp619His | p.D619H | P78527 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response | |
| PRKDC | SNV | Missense_Mutation | novel | c.3658N>G | p.Leu1220Val | p.L1220V | P78527 | protein_coding | deleterious(0.01) | possibly_damaging(0.622) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| PRKDC | SNV | Missense_Mutation | novel | c.1504N>A | p.Glu502Lys | p.E502K | P78527 | protein_coding | tolerated(0.18) | benign(0.076) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| PRKDC | SNV | Missense_Mutation | novel | c.5396N>G | p.Glu1799Gly | p.E1799G | P78527 | protein_coding | tolerated(0.13) | benign(0.118) | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| PRKDC | SNV | Missense_Mutation | c.9458C>G | p.Ser3153Cys | p.S3153C | P78527 | protein_coding | deleterious(0) | possibly_damaging(0.907) | TCGA-A7-A13D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| PRKDC | SNV | Missense_Mutation | novel | c.5745N>C | p.Leu1915Phe | p.L1915F | P78527 | protein_coding | deleterious(0) | probably_damaging(0.914) | TCGA-A7-A6VV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | CR |
| PRKDC | SNV | Missense_Mutation | c.2706A>T | p.Lys902Asn | p.K902N | P78527 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A7-A6VX-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | CR | |
| PRKDC | SNV | Missense_Mutation | c.2210N>T | p.Pro737Leu | p.P737L | P78527 | protein_coding | deleterious(0.01) | benign(0.354) | TCGA-A8-A099-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | exemestane | SD | |
| PRKDC | SNV | Missense_Mutation | c.6367N>T | p.Pro2123Ser | p.P2123S | P78527 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PRKDC | SNV | Missense_Mutation | c.3394N>A | p.Asp1132Asn | p.D1132N | P78527 | protein_coding | tolerated(0.21) | benign(0.055) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 |
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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 |
| 5591 | PRKDC | TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, ENZYME, PHOSPHATIDYLINOSITOL 3 KINASE, CLINICALLY ACTIONABLE | inhibitor | 252827496 | ||
| 5591 | PRKDC | TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, ENZYME, PHOSPHATIDYLINOSITOL 3 KINASE, CLINICALLY ACTIONABLE | M9831 | |||
| 5591 | PRKDC | TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, ENZYME, PHOSPHATIDYLINOSITOL 3 KINASE, CLINICALLY ACTIONABLE | KU-0060648 | CHEMBL1086377 | 23855836 | |
| 5591 | PRKDC | TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, ENZYME, PHOSPHATIDYLINOSITOL 3 KINASE, CLINICALLY ACTIONABLE | inhibitor | 178102582 | ||
| 5591 | PRKDC | TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, ENZYME, PHOSPHATIDYLINOSITOL 3 KINASE, CLINICALLY ACTIONABLE | inhibitor | 249565693 | ||
| 5591 | PRKDC | TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, ENZYME, PHOSPHATIDYLINOSITOL 3 KINASE, CLINICALLY ACTIONABLE | inhibitor | 354702239 | ||
| 5591 | PRKDC | TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, ENZYME, PHOSPHATIDYLINOSITOL 3 KINASE, CLINICALLY ACTIONABLE | inhibitor | 178102681 | WORTMANNIN | |
| 5591 | PRKDC | TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, ENZYME, PHOSPHATIDYLINOSITOL 3 KINASE, CLINICALLY ACTIONABLE | SF1126 | |||
| 5591 | PRKDC | TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, ENZYME, PHOSPHATIDYLINOSITOL 3 KINASE, CLINICALLY ACTIONABLE | inhibitor | 249565692 | ||
| 5591 | PRKDC | TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, ENZYME, PHOSPHATIDYLINOSITOL 3 KINASE, CLINICALLY ACTIONABLE | inhibitor | 404859048 |
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