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Gene: PARN |
Gene summary for PARN |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PARN | Gene ID | 5073 |
| Gene name | poly(A)-specific ribonuclease | |
| Gene Alias | DAN | |
| Cytomap | 16p13.12 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | B3KN69 |
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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 |
| 5073 | PARN | CCI_2 | Human | Cervix | CC | 1.77e-06 | 6.79e-01 | 0.5249 |
| 5073 | PARN | CCI_3 | Human | Cervix | CC | 5.32e-03 | 5.01e-01 | 0.516 |
| 5073 | PARN | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.28e-03 | 5.37e-01 | 0.281 |
| 5073 | PARN | A015-C-203 | Human | Colorectum | FAP | 1.77e-12 | -2.66e-01 | -0.1294 |
| 5073 | PARN | A002-C-201 | Human | Colorectum | FAP | 4.61e-05 | -2.56e-01 | 0.0324 |
| 5073 | PARN | A001-C-108 | Human | Colorectum | FAP | 5.11e-06 | -1.68e-01 | -0.0272 |
| 5073 | PARN | A002-C-205 | Human | Colorectum | FAP | 7.90e-09 | -2.06e-01 | -0.1236 |
| 5073 | PARN | A015-C-006 | Human | Colorectum | FAP | 5.72e-06 | -1.60e-01 | -0.0994 |
| 5073 | PARN | A015-C-106 | Human | Colorectum | FAP | 3.45e-07 | -1.40e-01 | -0.0511 |
| 5073 | PARN | A002-C-114 | Human | Colorectum | FAP | 4.12e-08 | -2.49e-01 | -0.1561 |
| 5073 | PARN | A015-C-104 | Human | Colorectum | FAP | 5.23e-13 | -2.82e-01 | -0.1899 |
| 5073 | PARN | A001-C-014 | Human | Colorectum | FAP | 7.88e-06 | -1.78e-01 | 0.0135 |
| 5073 | PARN | A002-C-016 | Human | Colorectum | FAP | 7.22e-12 | -2.23e-01 | 0.0521 |
| 5073 | PARN | A015-C-002 | Human | Colorectum | FAP | 3.47e-04 | -2.28e-01 | -0.0763 |
| 5073 | PARN | A001-C-203 | Human | Colorectum | FAP | 2.21e-04 | 5.73e-03 | -0.0481 |
| 5073 | PARN | A002-C-116 | Human | Colorectum | FAP | 5.15e-17 | -2.31e-01 | -0.0452 |
| 5073 | PARN | A014-C-008 | Human | Colorectum | FAP | 2.25e-04 | -2.51e-01 | -0.191 |
| 5073 | PARN | A018-E-020 | Human | Colorectum | FAP | 2.49e-08 | -2.30e-01 | -0.2034 |
| 5073 | PARN | F034 | Human | Colorectum | FAP | 1.42e-09 | -1.92e-01 | -0.0665 |
| 5073 | PARN | CRC-1-8810 | Human | Colorectum | CRC | 1.69e-02 | 7.61e-02 | 0.6257 |
| 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 | ||
| 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 | ||
| 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 | ||
| 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:00905012 | Oral cavity | OSCC | RNA phosphodiester bond hydrolysis | 95/7305 | 152/18723 | 3.65e-09 | 8.22e-08 | 95 |
| GO:00311232 | Oral cavity | OSCC | RNA 3'-end processing | 75/7305 | 116/18723 | 1.93e-08 | 3.79e-07 | 75 |
| GO:00001845 | Oral cavity | OSCC | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 31/7305 | 37/18723 | 2.80e-08 | 5.41e-07 | 31 |
| GO:00718979 | Oral cavity | OSCC | DNA biosynthetic process | 106/7305 | 180/18723 | 4.86e-08 | 8.95e-07 | 106 |
| GO:003220410 | Oral cavity | OSCC | regulation of telomere maintenance | 55/7305 | 80/18723 | 6.67e-08 | 1.19e-06 | 55 |
| GO:00610149 | Oral cavity | OSCC | positive regulation of mRNA catabolic process | 58/7305 | 87/18723 | 1.59e-07 | 2.61e-06 | 58 |
| GO:00903052 | Oral cavity | OSCC | nucleic acid phosphodiester bond hydrolysis | 142/7305 | 261/18723 | 2.90e-07 | 4.43e-06 | 142 |
| GO:200027817 | Oral cavity | OSCC | regulation of DNA biosynthetic process | 67/7305 | 106/18723 | 3.85e-07 | 5.75e-06 | 67 |
| GO:00611579 | Oral cavity | OSCC | mRNA destabilization | 55/7305 | 84/18723 | 8.05e-07 | 1.12e-05 | 55 |
| GO:00507799 | Oral cavity | OSCC | RNA destabilization | 57/7305 | 88/18723 | 8.70e-07 | 1.19e-05 | 57 |
| GO:00094511 | Oral cavity | OSCC | RNA modification | 95/7305 | 167/18723 | 2.05e-06 | 2.62e-05 | 95 |
| GO:000700410 | Oral cavity | OSCC | telomere maintenance via telomerase | 46/7305 | 69/18723 | 3.00e-06 | 3.66e-05 | 46 |
| GO:200057316 | Oral cavity | OSCC | positive regulation of DNA biosynthetic process | 44/7305 | 66/18723 | 4.91e-06 | 5.57e-05 | 44 |
| GO:200125216 | Oral cavity | OSCC | positive regulation of chromosome organization | 52/7305 | 82/18723 | 6.56e-06 | 7.24e-05 | 52 |
| GO:19048726 | Oral cavity | OSCC | regulation of telomerase RNA localization to Cajal body | 16/7305 | 18/18723 | 1.75e-05 | 1.71e-04 | 16 |
| GO:001083316 | Oral cavity | OSCC | telomere maintenance via telomere lengthening | 50/7305 | 81/18723 | 2.87e-05 | 2.64e-04 | 50 |
| GO:00906706 | Oral cavity | OSCC | RNA localization to Cajal body | 16/7305 | 19/18723 | 7.05e-05 | 5.60e-04 | 16 |
| GO:00906716 | Oral cavity | OSCC | telomerase RNA localization to Cajal body | 16/7305 | 19/18723 | 7.05e-05 | 5.60e-04 | 16 |
| GO:00906726 | Oral cavity | OSCC | telomerase RNA localization | 16/7305 | 19/18723 | 7.05e-05 | 5.60e-04 | 16 |
| GO:00906856 | Oral cavity | OSCC | RNA localization to nucleus | 16/7305 | 19/18723 | 7.05e-05 | 5.60e-04 | 16 |
| 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 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0301824 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
| hsa0301834 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
| hsa030189 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
| hsa0301814 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
| hsa0301841 | Oral cavity | EOLP | RNA degradation | 22/1218 | 79/8465 | 1.33e-03 | 4.80e-03 | 2.83e-03 | 22 |
| hsa0301851 | Oral cavity | EOLP | RNA degradation | 22/1218 | 79/8465 | 1.33e-03 | 4.80e-03 | 2.83e-03 | 22 |
| hsa0301861 | Oral cavity | NEOLP | RNA degradation | 18/1112 | 79/8465 | 1.25e-02 | 4.06e-02 | 2.56e-02 | 18 |
| hsa0301871 | Oral cavity | NEOLP | RNA degradation | 18/1112 | 79/8465 | 1.25e-02 | 4.06e-02 | 2.56e-02 | 18 |
| 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 |
| PARN | SNV | Missense_Mutation | rs766730789 | c.1416N>C | p.Gln472His | p.Q472H | O95453 | protein_coding | tolerated(0.31) | benign(0.001) | TCGA-C8-A12K-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PARN | insertion | Frame_Shift_Ins | novel | c.244_245insGGTTT | p.Lys82ArgfsTer5 | p.K82Rfs*5 | O95453 | protein_coding | TCGA-A8-A07U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD | ||
| PARN | insertion | Nonsense_Mutation | novel | c.243_244insGAGACAGACAGACAGATATGAGAACATG | p.Lys82GlufsTer7 | p.K82Efs*7 | O95453 | protein_coding | TCGA-A8-A07U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD | ||
| PARN | SNV | Missense_Mutation | c.1805N>T | p.Ser602Leu | p.S602L | O95453 | protein_coding | tolerated_low_confidence(0.25) | benign(0) | TCGA-BI-A0VR-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PARN | SNV | Missense_Mutation | novel | c.82N>C | p.Asp28His | p.D28H | O95453 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD |
| PARN | SNV | Missense_Mutation | novel | c.1504N>C | p.Glu502Gln | p.E502Q | O95453 | protein_coding | tolerated(0.07) | possibly_damaging(0.645) | TCGA-HM-A4S6-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
| PARN | insertion | Frame_Shift_Ins | novel | c.195_196insAGGAT | p.Leu66ArgfsTer21 | p.L66Rfs*21 | O95453 | protein_coding | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD | ||
| PARN | SNV | Missense_Mutation | c.1423N>C | p.Trp475Arg | p.W475R | O95453 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PARN | SNV | Missense_Mutation | novel | c.211N>A | p.Leu71Ile | p.L71I | O95453 | protein_coding | deleterious(0.01) | possibly_damaging(0.716) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| PARN | SNV | Missense_Mutation | c.1557G>T | p.Glu519Asp | p.E519D | O95453 | protein_coding | tolerated(0.24) | benign(0.006) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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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