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Gene: PRKN |
Gene summary for PRKN |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PRKN | Gene ID | 5071 |
| Gene name | parkin RBR E3 ubiquitin protein ligase | |
| Gene Alias | AR-JP | |
| Cytomap | 6q26 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | O60260 |
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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 |
| 5071 | PRKN | HTA11_3410_2000001011 | Human | Colorectum | AD | 3.72e-13 | -5.10e-01 | 0.0155 |
| 5071 | PRKN | HTA11_347_2000001011 | Human | Colorectum | AD | 1.03e-03 | 4.89e-01 | -0.1954 |
| 5071 | PRKN | HTA11_5212_2000001011 | Human | Colorectum | AD | 8.75e-03 | -6.73e-01 | -0.2061 |
| 5071 | PRKN | HTA11_866_3004761011 | Human | Colorectum | AD | 7.71e-13 | -5.68e-01 | 0.096 |
| 5071 | PRKN | HTA11_8622_2000001021 | Human | Colorectum | SER | 3.72e-02 | -4.72e-01 | 0.0528 |
| 5071 | PRKN | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.23e-02 | -3.73e-01 | 0.0674 |
| 5071 | PRKN | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.08e-70 | -1.11e+00 | 0.294 |
| 5071 | PRKN | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.29e-02 | -1.11e+00 | 0.3487 |
| 5071 | PRKN | HTA11_99999965104_69814 | Human | Colorectum | MSS | 4.40e-25 | -1.11e+00 | 0.281 |
| 5071 | PRKN | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.63e-63 | -1.11e+00 | 0.3859 |
| 5071 | PRKN | HTA11_99999973899_84307 | Human | Colorectum | MSS | 8.83e-20 | -1.11e+00 | 0.2585 |
| 5071 | PRKN | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.09e-63 | -1.11e+00 | 0.3005 |
| 5071 | PRKN | A001-C-207 | Human | Colorectum | FAP | 3.66e-03 | -3.81e-01 | 0.1278 |
| 5071 | PRKN | A015-C-203 | Human | Colorectum | FAP | 3.17e-24 | -4.62e-01 | -0.1294 |
| 5071 | PRKN | A015-C-204 | Human | Colorectum | FAP | 1.58e-02 | -2.43e-01 | -0.0228 |
| 5071 | PRKN | A014-C-040 | Human | Colorectum | FAP | 6.56e-08 | -7.94e-01 | -0.1184 |
| 5071 | PRKN | A002-C-201 | Human | Colorectum | FAP | 1.46e-18 | -6.31e-01 | 0.0324 |
| 5071 | PRKN | A001-C-119 | Human | Colorectum | FAP | 2.81e-09 | -5.94e-01 | -0.1557 |
| 5071 | PRKN | A001-C-108 | Human | Colorectum | FAP | 2.00e-17 | -5.19e-01 | -0.0272 |
| 5071 | PRKN | A002-C-205 | Human | Colorectum | FAP | 4.68e-27 | -7.19e-01 | -0.1236 |
| Page: 1 2 3 4 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma |
| ∗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:00108211 | Colorectum | SER | regulation of mitochondrion organization | 48/2897 | 144/18723 | 7.51e-08 | 4.70e-06 | 48 |
| GO:00516561 | Colorectum | SER | establishment of organelle localization | 100/2897 | 390/18723 | 1.11e-07 | 6.79e-06 | 100 |
| GO:00323861 | Colorectum | SER | regulation of intracellular transport | 89/2897 | 337/18723 | 1.34e-07 | 7.96e-06 | 89 |
| GO:00508211 | Colorectum | SER | protein stabilization | 58/2897 | 191/18723 | 1.46e-07 | 8.59e-06 | 58 |
| GO:00324341 | Colorectum | SER | regulation of proteasomal ubiquitin-dependent protein catabolic process | 45/2897 | 134/18723 | 1.48e-07 | 8.67e-06 | 45 |
| GO:00313961 | Colorectum | SER | regulation of protein ubiquitination | 62/2897 | 210/18723 | 1.69e-07 | 9.71e-06 | 62 |
| GO:00162361 | Colorectum | SER | macroautophagy | 79/2897 | 291/18723 | 1.97e-07 | 1.10e-05 | 79 |
| GO:00106391 | Colorectum | SER | negative regulation of organelle organization | 90/2897 | 348/18723 | 3.14e-07 | 1.69e-05 | 90 |
| GO:00705851 | Colorectum | SER | protein localization to mitochondrion | 42/2897 | 125/18723 | 3.75e-07 | 1.98e-05 | 42 |
| GO:20012341 | Colorectum | SER | negative regulation of apoptotic signaling pathway | 64/2897 | 224/18723 | 3.98e-07 | 2.06e-05 | 64 |
| GO:00323881 | Colorectum | SER | positive regulation of intracellular transport | 59/2897 | 202/18723 | 4.98e-07 | 2.48e-05 | 59 |
| GO:00621971 | Colorectum | SER | cellular response to chemical stress | 87/2897 | 337/18723 | 5.33e-07 | 2.59e-05 | 87 |
| GO:20012431 | Colorectum | SER | negative regulation of intrinsic apoptotic signaling pathway | 35/2897 | 98/18723 | 6.73e-07 | 3.23e-05 | 35 |
| GO:19901821 | Colorectum | SER | exosomal secretion | 13/2897 | 20/18723 | 7.51e-07 | 3.57e-05 | 13 |
| GO:00096361 | Colorectum | SER | response to toxic substance | 71/2897 | 262/18723 | 8.63e-07 | 4.07e-05 | 71 |
| GO:19054751 | Colorectum | SER | regulation of protein localization to membrane | 52/2897 | 175/18723 | 1.31e-06 | 6.04e-05 | 52 |
| GO:19031461 | Colorectum | SER | regulation of autophagy of mitochondrion | 17/2897 | 33/18723 | 1.53e-06 | 6.86e-05 | 17 |
| GO:19029041 | Colorectum | SER | negative regulation of supramolecular fiber organization | 50/2897 | 167/18723 | 1.63e-06 | 7.23e-05 | 50 |
| GO:19018001 | Colorectum | SER | positive regulation of proteasomal protein catabolic process | 38/2897 | 114/18723 | 1.65e-06 | 7.23e-05 | 38 |
| GO:00977341 | Colorectum | SER | extracellular exosome biogenesis | 13/2897 | 21/18723 | 1.69e-06 | 7.35e-05 | 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 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05012 | Colorectum | AD | Parkinson disease | 147/2092 | 266/8465 | 2.53e-27 | 8.48e-25 | 5.41e-25 | 147 |
| hsa05014 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
| hsa05022 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
| hsa04141 | Colorectum | AD | Protein processing in endoplasmic reticulum | 80/2092 | 174/8465 | 5.96e-10 | 1.25e-08 | 7.96e-09 | 80 |
| hsa04120 | Colorectum | AD | Ubiquitin mediated proteolysis | 58/2092 | 142/8465 | 1.46e-05 | 1.53e-04 | 9.76e-05 | 58 |
| hsa04137 | Colorectum | AD | Mitophagy - animal | 29/2092 | 72/8465 | 2.49e-03 | 1.35e-02 | 8.59e-03 | 29 |
| hsa050121 | Colorectum | AD | Parkinson disease | 147/2092 | 266/8465 | 2.53e-27 | 8.48e-25 | 5.41e-25 | 147 |
| hsa050141 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
| hsa050221 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
| hsa041411 | Colorectum | AD | Protein processing in endoplasmic reticulum | 80/2092 | 174/8465 | 5.96e-10 | 1.25e-08 | 7.96e-09 | 80 |
| hsa041201 | Colorectum | AD | Ubiquitin mediated proteolysis | 58/2092 | 142/8465 | 1.46e-05 | 1.53e-04 | 9.76e-05 | 58 |
| hsa041371 | Colorectum | AD | Mitophagy - animal | 29/2092 | 72/8465 | 2.49e-03 | 1.35e-02 | 8.59e-03 | 29 |
| hsa050222 | Colorectum | SER | Pathways of neurodegeneration - multiple diseases | 168/1580 | 476/8465 | 6.23e-19 | 2.07e-17 | 1.50e-17 | 168 |
| hsa050142 | Colorectum | SER | Amyotrophic lateral sclerosis | 138/1580 | 364/8465 | 9.89e-19 | 2.99e-17 | 2.17e-17 | 138 |
| hsa041412 | Colorectum | SER | Protein processing in endoplasmic reticulum | 60/1580 | 174/8465 | 4.20e-07 | 7.33e-06 | 5.32e-06 | 60 |
| hsa041202 | Colorectum | SER | Ubiquitin mediated proteolysis | 39/1580 | 142/8465 | 6.18e-03 | 3.66e-02 | 2.66e-02 | 39 |
| hsa050223 | Colorectum | SER | Pathways of neurodegeneration - multiple diseases | 168/1580 | 476/8465 | 6.23e-19 | 2.07e-17 | 1.50e-17 | 168 |
| hsa050143 | Colorectum | SER | Amyotrophic lateral sclerosis | 138/1580 | 364/8465 | 9.89e-19 | 2.99e-17 | 2.17e-17 | 138 |
| hsa041413 | Colorectum | SER | Protein processing in endoplasmic reticulum | 60/1580 | 174/8465 | 4.20e-07 | 7.33e-06 | 5.32e-06 | 60 |
| hsa041203 | Colorectum | SER | Ubiquitin mediated proteolysis | 39/1580 | 142/8465 | 6.18e-03 | 3.66e-02 | 2.66e-02 | 39 |
| Page: 1 2 3 4 5 |
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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 |
| Page: 1 |
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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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