Table 2.
Altered Pathways by Deregulated miR in Ovarian Cancer.
| A. KEGG Pathways Regulated by Rpregulated miR | ||||
|---|---|---|---|---|
| S.No. | Name | Hits | p-Value | Adj. p-Value |
| 1 | Pathways in cancer | 36 | 1.76 × 10−12 | 1.76 × 10−10 |
| 2 | Chronic myeloid leukemia | 18 | 3.93 × 10−12 | 1.97 × 10−10 |
| 3 | Prostate cancer | 18 | 9.44 × 10−11 | 3.15 × 10−09 |
| 4 | p53 signaling pathway | 16 | 1.44 × 10−10 | 3.60 × 10−09 |
| 5 | Bladder cancer | 11 | 4.30 × 10−10 | 8.60 × 10−09 |
| 6 | Glioma | 14 | 7.53 × 10−09 | 1.26 × 10−07 |
| 7 | Pancreatic cancer | 14 | 1.71 × 10−08 | 2.44 × 10−07 |
| 8 | Cell cycle | 18 | 3.73 × 10−08 | 4.66 × 10−07 |
| 9 | Adherens junction | 13 | 1.73 × 10−07 | 1.92 × 10−06 |
| 10 | Melanoma | 12 | 9.43 × 10−07 | 9.43 × 10−06 |
| B. Gene Ontology Enrichment for Biological Process (GO-BP) Regulated by Upregulated miR | ||||
| S.No. | Name | Hits | p-Value | Adj. p-Value |
| 1 | G1 phase of mitotic cell cycle | 11 | 7.03 × 10−08 | 5.6 × 10−06 |
| 2 | G1 phase | 11 | 1.12 × 10−07 | 5.6 × 10−06 |
| 3 | Gland development | 27 | 2.20 × 10−07 | 5.98 × 10−06 |
| 4 | Negative regulation of transcription from RNA polymerase II promoter | 39 | 2.39 × 10−07 | 5.98 × 10−06 |
| 5 | Regulation of cell proliferation | 72 | 1.72 × 10−06 | 3.44 × 10−05 |
| 6 | Negative regulation of transcription, DNA-dependent | 54 | 4.07 × 10−06 | 4.67 × 10−05 |
| 7 | Response to ionizing radiation | 54 | 4.07 × 10−06 | 4.67 × 10−05 |
| 8 | Negative regulation of cellular biosynthetic process | 14 | 4.16 × 10−06 | 4.67 × 10−05 |
| 9 | Negative regulation of RNA metabolic process | 63 | 4.2 × 10−06 | 4.67 × 10−05 |
| 10 | Negative regulation of nucleobase-containing compound metabolic process | 55 | 5.68 × 10−06 | 5.45 × 10−05 |
| C. Gene Ontology Enrichment for Molecular Function (GO-MF) Regulated by Upregulated miR | ||||
| S. No. | Name | Hits | p-Value | Adj. p-Value |
| 1 | Negative regulation of transcription, DNA-dependent | 54 | 1.02 × 10−06 | 0.000102 |
| 2 | Double-stranded DNA binding | 16 | 3.64 × 10−06 | 0.000182 |
| 3 | Structure-specific DNA binding | 20 | 1.31 × 10−05 | 0.00033 |
| 4 | Sequence-specific DNA binding | 41 | 1.32 × 10−05 | 0.00033 |
| 5 | RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity | 12 | 5.13 × 10−05 | 0.00096 |
| 6 | Transcription from RNA polymerase II promoter | 81 | 6.07 × 10−05 | 0.00096 |
| 7 | Enzyme binding | 56 | 6.74 × 10−05 | 0.00096 |
| 8 | DNA binding | 107 | 8.38 × 10−05 | 0.00096 |
| 9 | Phosphatase binding | 12 | 8.64 × 10−05 | 0.00096 |
| 10 | Chromatin binding | 22 | 0.000184 | 0.001608 |
| D. KEGG Pathways Regulated by Downregulated miR | ||||
| S. No. | Name | Hits | p-Value | Adj. p-Value |
| 1 | Pathways in cancer | 64 | 1.45 × 10−18 | 1.45 × 10−16 |
| 2 | Prostate cancer | 31 | 2.65 × 10−16 | 1.33 × 10−14 |
| 3 | Chronic myeloid leukemia | 26 | 7.80 × 10−14 | 2.60 × 10−12 |
| 4 | Small cell lung cancer | 26 | 9.30 × 10−13 | 2.33 × 10−11 |
| 5 | Glioma | 22 | 2.27 × 10−11 | 4.54 × 10−10 |
| 6 | P53 signaling pathway | 22 | 6.30 × 10−11 | 1.05 × 10−09 |
| 7 | Pancreatic cancer | 22 | 8.72 × 10−11 | 1.25 × 10−09 |
| 8 | Cell cycle | 29 | 3.71 × 10−10 | 4.64 × 10−09 |
| 9 | HTLV-I infection | 37 | 1.41 × 10−09 | 1.57 × 10−08 |
| 10 | Melanoma | 20 | 3.22 × 10−09 | 3.22 × 10−08 |
| E. Geneontology Enrichment for Biological Process (GO-BP) Regulated by Downregulated miR | ||||
| S. No. | Name | Hits | p-Value | Adj. p-Value |
| 1 | Negative regulation of transcription from RNA polymerase II promoter | 74 | 2.97 × 10−11 | 2.97 × 10−09 |
| 2 | Interphase of mitotic cell cycle | 59 | 2.11 × 10−09 | 1.06 × 10−07 |
| 3 | Interphase | 59 | 4.22 × 10−09 | 1.41 × 10−07 |
| 4 | Negative regulation of RNA metabolic process | 105 | 1.76 × 10−08 | 3.22 × 10−07 |
| 5 | Negative regulation of transcription, DNA-dependent | 102 | 1.93 × 10−08 | 3.22 × 10−07 |
| 6 | Negative regulation of cellular metabolic process | 102 | 1.93 × 10−08 | 3.22 × 10−07 |
| 7 | Regulation of cell cycle | 151 | 4.11 × 10−08 | 5.23 × 10−07 |
| 8 | Regulation of transcription from RNA polymerase II promoter | 93 | 4.18 × 10−08 | 5.23 × 10−07 |
| 9 | Negative regulation of cellular biosynthetic process | 146 | 7.03 × 10−08 | 7.81 × 10−07 |
| 10 | Negative regulation of metabolic process | 117 | 1.14 × 10−07 | 1.14 × 10−06 |
| F. Gene Ontology Enrichment for Molecular Function (GO-MF) Regulated by Downregulated miR | ||||
| S. No. | Name | Hits | p-Value | Adj. p-Value |
| 1 | Negative regulation of transcription, DNA-dependent | 102 | 1.72 × 10−09 | 1.72 × 10−07 |
| 2 | Transcription from RNA polymerase II promoter | 167 | 6.75 × 10−09 | 2.40 × 10−07 |
| 3 | Transcription factor binding | 62 | 9.59 × 10−09 | 2.40 × 10−07 |
| 4 | Enzyme binding | 115 | 1.11 × 10−08 | 2.40 × 10−07 |
| 5 | Kinase binding | 54 | 1.20 × 10−08 | 2.40 × 10−07 |
| 6 | Protein kinase binding | 48 | 1.14 × 10−07 | 1.9 × 10−06 |
| 7 | Positive regulation of transcription, DNA-dependent | 111 | 1.5 × 10−06 | 2.14 × 10−05 |
| 8 | Nucleotide binding | 191 | 2.08 × 10−06 | 0.000026 |
| 9 | SMAD binding | 15 | 4.8 × 10−06 | 5.33 × 10−05 |
| 10 | Phosphatase binding | 20 | 7.74 × 10−06 | 7.74 × 10−05 |
Pathway enrichment analysis for deregulated miR in ovarian cancer: Gene targets for miR were predicted using miRNet web tool (https://www.mirnet.ca/) and miRTarBase v8.0. (A,D) KEGG pathway analysis enrichment, gene ontology enrichment for (B,E) biological process (GO-BP) and (C,F) molecular function (GO-MF) were analyzed for upregulated (A–C) and downregulated (D–F) miR target genes; the 10 most significant pathways based on the network generated using degree cutoff 5 are shown.