This regulatory network was inferred from the input dataset. The miRNAs and mRNAs are
presented as round and rectangle nodes respectively. The numerical value popped up upon mouse over the gene node is the log2 transformed fold-change of the gene expression between the two groups. All of the nodes are clickable, and the detailed information of the miRNAs/mRNAs and related cancer pathway will be displayed in another window. The edges between nodes are supported by both interactions (predicted or experimentally verified) and correlations learnt from cancer dataset. The numerical value popped up upon mouse over the edge is the correlation beat value (effect size) between the two nodes. The experimental evidences of the edges reported in previous cancer studies are highlighted by red/orange color. All of these information can be accessed by the "mouse-over" action. This network shows a full map of the miRNA-mRNA regulation of the input gene list(s), and the hub miRNAs (with the high network degree/betweenness centrality) would be the potential cancer drivers or tumor suppressors. The full result table can be accessed in the "Regulations" tab.
"miRNACancerMAP" is also a network visualization tool for users to draw their regulatory network by personal customization. Users can set the complexity of the network by limiting the number of nodes or edges. And the color of the nodes can be defined by different categories of the mRNAs and miRNAs, such as Gene-Ontology, pathway, and expression status. Users can also select to use network degree or network betweenness centrality to define the node size. And edges can be black or colored by the correlation. Purple edge means negative correlation (mostly found between miRNA and mRNA), and blue edge means positive correlation (found in PPI or miRNA-miRNA sponge effect). We can also add the protein-protein interactions (PPI) into the network. This result will show the cluster of genes regulated by some specific miRNAs. Additionally, miRNA-miRNA edges can be added by the "miRNA sponge" button, presenting some clusters of miRNAs that have the interactions via sponge effect.
| Num | microRNA | Gene | miRNA log2FC | miRNA pvalue | Gene log2FC | Gene pvalue | Interaction | Correlation beta | Correlation P-value | PMID | Reported in cancer studies |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | hsa-miR-103a-3p | CD274 | 0.99 | 0.00468 | 2.22 | 0.05161 | miRNAWalker2 validate | -0.48 | 0.01013 | NA | |
| 2 | hsa-miR-106a-5p | CD274 | 3.99 | 0 | 2.22 | 0.05161 | MirTarget; miRNATAP | -0.24 | 0.00245 | NA | |
| 3 | hsa-miR-182-5p | CD274 | 5.87 | 0 | 2.22 | 0.05161 | mirMAP | -0.34 | 5.0E-5 | NA | |
| 4 | hsa-miR-200a-3p | CD274 | 6.34 | 0 | 2.22 | 0.05161 | MirTarget | -0.35 | 1.0E-5 | NA | |
| 5 | hsa-miR-20b-5p | CD274 | 4.57 | 5.0E-5 | 2.22 | 0.05161 | MirTarget; miRNATAP | -0.19 | 0.0007 | 24468585 | These findings suggest that miR-20b -21 and -130b up-regulated in colorectal cancer through inhibiting the expression of PTEN result in B7-H1 over-expression in colorectal cancer |
| 6 | hsa-miR-324-5p | CD274 | 1.31 | 0.01168 | 2.22 | 0.05161 | miRanda | -0.47 | 0.00014 | NA | |
| 7 | hsa-miR-429 | CD274 | 6.4 | 0 | 2.22 | 0.05161 | miRanda | -0.41 | 0 | NA | |
| 8 | hsa-miR-497-5p | CD274 | -1.44 | 0.02251 | 2.22 | 0.05161 | MirTarget | -0.38 | 0.00018 | NA | |
| 9 | hsa-miR-93-5p | CD274 | 2.66 | 0 | 2.22 | 0.05161 | MirTarget; miRNATAP | -0.46 | 0.00064 | NA | |
| 10 | hsa-miR-107 | EGFR | 1.49 | 0.00013 | 1.4 | 0.17026 | miRanda | -0.37 | 0.012 | NA | |
| 11 | hsa-miR-125a-5p | EGFR | -1.32 | 0.00714 | 1.4 | 0.17026 | mirMAP | -0.42 | 0.00032 | 19881956; 27094723; 24484870 | We report that EGFR signaling leads to transcriptional repression of the miRNA miR-125a through the ETS family transcription factor PEA3;Suppression of microRNA 125a 5p upregulates the TAZ EGFR signaling pathway and promotes retinoblastoma proliferation; Moreover the overexpression of miR-125a-5p led to a decrease in TAZ expression and downstream EGFR signaling pathway activation both in vitro and vivo; Finally TAZ overexpression in retinoblastoma cells overexpressing miR-125a-5p restored retinoblastoma cell proliferation and EGFR pathway activation; Taken together our data demonstrated that miR-125a-5p functions as an important tumor suppressor that suppresses the EGFR pathway by targeting TAZ to inhibit tumor progression in retinoblastoma;miR 125a regulates cell cycle proliferation and apoptosis by targeting the ErbB pathway in acute myeloid leukemia; Profiling revealed the ErbB pathway as significantly decreased with ectopic miR-125a; Either ectopic expression of miR-125a or inhibition of ErbB via Mubritinib resulted in inhibition of cell cycle proliferation and progression with enhanced apoptosis revealing ErbB inhibitors as potential novel therapeutic agents for treating miR-125a-low AML |
| 12 | hsa-miR-128-3p | EGFR | 1.36 | 0.00408 | 1.4 | 0.17026 | miRNAWalker2 validate; miRTarBase | -0.33 | 0.00791 | NA | |
| 13 | hsa-miR-141-3p | EGFR | 7.3 | 0 | 1.4 | 0.17026 | MirTarget | -0.16 | 0.03017 | 26025929 | Treatment with the EGFR inhibitor AG1478 or overexpression of miR141 blocked the activity of ERK downstream of EGFR and inhibited KLF8-depndent cell invasiveness proliferation and viability in cell culture and invasive growth and lung metastasis in nude mice |
| 14 | hsa-miR-148b-5p | EGFR | 2.81 | 0 | 1.4 | 0.17026 | mirMAP | -0.29 | 0.00994 | NA | |
| 15 | hsa-miR-186-5p | EGFR | 0.45 | 0.18545 | 1.4 | 0.17026 | mirMAP | -0.73 | 3.0E-5 | NA | |
| 16 | hsa-miR-188-5p | EGFR | 1.39 | 0.02516 | 1.4 | 0.17026 | mirMAP | -0.26 | 0.00496 | NA | |
| 17 | hsa-miR-192-3p | EGFR | 0.85 | 0.48094 | 1.4 | 0.17026 | mirMAP | -0.2 | 6.0E-5 | NA | |
| 18 | hsa-miR-192-5p | EGFR | 1.78 | 0.11349 | 1.4 | 0.17026 | mirMAP | -0.25 | 0 | NA | |
| 19 | hsa-miR-194-3p | EGFR | 1.92 | 0.10538 | 1.4 | 0.17026 | MirTarget | -0.18 | 0.00021 | NA | |
| 20 | hsa-miR-200a-3p | EGFR | 6.34 | 0 | 1.4 | 0.17026 | MirTarget | -0.31 | 1.0E-5 | 26184032; 19671845 | MicroRNA 200a Targets EGFR and c Met to Inhibit Migration Invasion and Gefitinib Resistance in Non Small Cell Lung Cancer; In this study we found that miR-200a is downregulated in NSCLC cells where it directly targets the 3'-UTR of both EGFR and c-Met mRNA; Overexpression of miR-200a in NSCLC cells significantly downregulates both EGFR and c-Met levels and severely inhibits cell migration and invasion;Protein expression and signaling pathway modulation as well as intracellular distribution of EGFR and ERRFI-1 were validated through Western blot analysis and confocal microscopy whereas ERRFI-1 direct target of miR-200 members was validated by using the wild-type and mutant 3'-untranslated region/ERRFI-1/luciferse reporters; We identified a tight association between the expression of miRNAs of the miR-200 family epithelial phenotype and sensitivity to EGFR inhibitors-induced growth inhibition in bladder carcinoma cell lines; The changes in EGFR sensitivity by silencing or forced expression of ERRFI-1 or by miR-200 expression have also been validated in additional cell lines UMUC5 and T24; Members of the miR-200 family appear to control the EMT process and sensitivity to EGFR therapy in bladder cancer cells and the expression of miR-200 is sufficient to restore EGFR dependency at least in some of the mesenchymal bladder cancer cells |
| 21 | hsa-miR-26b-3p | EGFR | 0.99 | 0.03514 | 1.4 | 0.17026 | mirMAP | -0.33 | 0.00731 | NA | |
| 22 | hsa-miR-29b-2-5p | EGFR | -0.6 | 0.18954 | 1.4 | 0.17026 | mirMAP | -0.65 | 0 | NA | |
| 23 | hsa-miR-30a-3p | EGFR | -1.22 | 0.16757 | 1.4 | 0.17026 | mirMAP | -0.21 | 0.00099 | NA | |
| 24 | hsa-miR-30a-5p | EGFR | -0.77 | 0.32049 | 1.4 | 0.17026 | miRNAWalker2 validate | -0.28 | 0.00021 | NA | |
| 25 | hsa-miR-30d-3p | EGFR | -0.07 | 0.85742 | 1.4 | 0.17026 | mirMAP | -0.36 | 0.01186 | NA | |
| 26 | hsa-miR-362-5p | EGFR | -1.22 | 0.04527 | 1.4 | 0.17026 | mirMAP | -0.43 | 0 | NA | |
| 27 | hsa-miR-375 | EGFR | 3.38 | 0.04499 | 1.4 | 0.17026 | miRanda | -0.22 | 0 | NA | |
| 28 | hsa-miR-3913-5p | EGFR | 0.15 | 0.73484 | 1.4 | 0.17026 | mirMAP | -0.33 | 0.01522 | NA | |
| 29 | hsa-miR-491-5p | EGFR | 0.57 | 0.31331 | 1.4 | 0.17026 | miRanda | -0.23 | 0.02883 | 25299770 | This latter effect is due to direct targeting of epidermal growth factor receptor EGFR by miR-491-5p and consequent inhibition of downstream AKT and MAPK signalling pathways; Induction of apoptosis by miR-491-5p in this cell line is mimicked by a combination of EGFR inhibition together with a BH3-mimetic molecule |
| 30 | hsa-miR-501-5p | EGFR | 1.04 | 0.07772 | 1.4 | 0.17026 | mirMAP | -0.25 | 0.01158 | NA | |
| 31 | hsa-miR-616-5p | EGFR | 2.48 | 0.00318 | 1.4 | 0.17026 | mirMAP | -0.17 | 0.04935 | NA | |
| 32 | hsa-miR-7-1-3p | EGFR | 1.43 | 0.00471 | 1.4 | 0.17026 | mirMAP | -0.48 | 3.0E-5 | NA | |
| 33 | hsa-miR-769-5p | EGFR | 0.42 | 0.34309 | 1.4 | 0.17026 | mirMAP | -0.3 | 0.02445 | NA | |
| 34 | hsa-miR-106b-5p | STAT3 | 2.81 | 0 | 0.02 | 0.95726 | miRNATAP | -0.11 | 0.00227 | 27325313 | We also found that EMMPRIN could down-regulate miR-106a and miR-106b expression in breast cancer cells which led to activating STAT3 and enhancing HIF-1α expression |
| 35 | hsa-miR-320b | STAT3 | 0.2 | 0.72722 | 0.02 | 0.95726 | miRanda | -0.11 | 0.00012 | NA | |
| 36 | hsa-miR-590-5p | STAT3 | 1.51 | 0.00239 | 0.02 | 0.95726 | miRanda; miRNATAP | -0.11 | 0.00092 | 27757042 | We found that the AKT/ERK and STAT3 signaling pathways were activated by miR-590-5p overexpression |
| 37 | hsa-miR-93-5p | STAT3 | 2.66 | 0 | 0.02 | 0.95726 | miRNAWalker2 validate; miRNATAP | -0.11 | 0.0016 | NA |
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|
| Num | Pathway | Pathview | Overlap | Size | P Value | Adj. P Value |
|---|
| Num | lncRNA | miRNAs | miRNAs count | Gene | Sponge regulatory network | lncRNA log2FC | lncRNA pvalue | Gene log2FC | Gene pvalue | lncRNA-gene Pearson correlation |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | RP11-498M15.1 | hsa-miR-107;hsa-miR-125a-5p;hsa-miR-128-3p;hsa-miR-186-5p;hsa-miR-188-5p;hsa-miR-192-3p;hsa-miR-192-5p;hsa-miR-194-3p;hsa-miR-29b-2-5p;hsa-miR-30a-3p;hsa-miR-30a-5p;hsa-miR-616-5p | 12 | EGFR | Sponge network | 7.388 | 0.02282 | 1.4 | 0.17026 | 0.559 |
| 2 | AC124789.1 | hsa-miR-107;hsa-miR-125a-5p;hsa-miR-128-3p;hsa-miR-141-3p;hsa-miR-192-3p;hsa-miR-194-3p;hsa-miR-200a-3p;hsa-miR-29b-2-5p;hsa-miR-362-5p;hsa-miR-3913-5p;hsa-miR-491-5p;hsa-miR-616-5p | 12 | EGFR | Sponge network | 1.298 | 0.42067 | 1.4 | 0.17026 | 0.535 |
| 3 | RP11-411K7.1 | hsa-miR-107;hsa-miR-125a-5p;hsa-miR-186-5p;hsa-miR-192-3p;hsa-miR-192-5p;hsa-miR-194-3p;hsa-miR-29b-2-5p;hsa-miR-30a-3p;hsa-miR-30a-5p;hsa-miR-30d-3p | 10 | EGFR | Sponge network | 4.154 | 0.00603 | 1.4 | 0.17026 | 0.507 |
| 4 | RP11-150O12.1 | hsa-miR-107;hsa-miR-125a-5p;hsa-miR-141-3p;hsa-miR-192-5p;hsa-miR-194-3p;hsa-miR-200a-3p;hsa-miR-29b-2-5p;hsa-miR-30a-3p;hsa-miR-30a-5p;hsa-miR-769-5p | 10 | EGFR | Sponge network | 1.864 | 0.30898 | 1.4 | 0.17026 | 0.483 |
| 5 | LINC00964 | hsa-miR-125a-5p;hsa-miR-192-3p;hsa-miR-192-5p;hsa-miR-194-3p;hsa-miR-200a-3p;hsa-miR-29b-2-5p;hsa-miR-30a-3p;hsa-miR-30a-5p;hsa-miR-30d-3p;hsa-miR-375 | 10 | EGFR | Sponge network | 6.695 | 0.0026 | 1.4 | 0.17026 | 0.463 |
| 6 | MIR205HG | hsa-miR-125a-5p;hsa-miR-192-3p;hsa-miR-192-5p;hsa-miR-194-3p;hsa-miR-29b-2-5p;hsa-miR-30a-3p;hsa-miR-30a-5p;hsa-miR-30d-3p;hsa-miR-362-5p;hsa-miR-616-5p | 10 | EGFR | Sponge network | 7.594 | 0.00251 | 1.4 | 0.17026 | 0.44 |
| 7 | AP001046.5 | hsa-miR-107;hsa-miR-125a-5p;hsa-miR-128-3p;hsa-miR-188-5p;hsa-miR-192-3p;hsa-miR-192-5p;hsa-miR-194-3p;hsa-miR-200a-3p;hsa-miR-30a-3p;hsa-miR-30d-3p | 10 | EGFR | Sponge network | 2.636 | 0.00941 | 1.4 | 0.17026 | 0.401 |
| 8 | AF131217.1 | hsa-miR-107;hsa-miR-141-3p;hsa-miR-192-3p;hsa-miR-192-5p;hsa-miR-194-3p;hsa-miR-200a-3p;hsa-miR-29b-2-5p;hsa-miR-375;hsa-miR-501-5p;hsa-miR-616-5p | 10 | EGFR | Sponge network | -1.542 | 0.34871 | 1.4 | 0.17026 | 0.347 |
| 9 | RP11-58E21.3 | hsa-miR-107;hsa-miR-125a-5p;hsa-miR-128-3p;hsa-miR-188-5p;hsa-miR-200a-3p;hsa-miR-30a-3p;hsa-miR-30a-5p;hsa-miR-30d-3p;hsa-miR-3913-5p;hsa-miR-769-5p | 10 | EGFR | Sponge network | 1.684 | 0.07749 | 1.4 | 0.17026 | 0.329 |
| 10 | GAS6-AS2 | hsa-miR-107;hsa-miR-128-3p;hsa-miR-141-3p;hsa-miR-186-5p;hsa-miR-192-3p;hsa-miR-192-5p;hsa-miR-194-3p;hsa-miR-200a-3p;hsa-miR-26b-3p;hsa-miR-7-1-3p | 10 | EGFR | Sponge network | -1.941 | 0.0681 | 1.4 | 0.17026 | 0.316 |
| 11 | RP11-567M16.1 | hsa-miR-107;hsa-miR-141-3p;hsa-miR-148b-5p;hsa-miR-186-5p;hsa-miR-192-3p;hsa-miR-192-5p;hsa-miR-200a-3p;hsa-miR-29b-2-5p;hsa-miR-30a-5p;hsa-miR-30d-3p;hsa-miR-616-5p;hsa-miR-769-5p | 12 | EGFR | Sponge network | -2.638 | 0.21408 | 1.4 | 0.17026 | 0.275 |
| 12 | RP11-276H19.1 | hsa-miR-107;hsa-miR-128-3p;hsa-miR-141-3p;hsa-miR-148b-5p;hsa-miR-186-5p;hsa-miR-192-3p;hsa-miR-192-5p;hsa-miR-194-3p;hsa-miR-200a-3p;hsa-miR-501-5p;hsa-miR-7-1-3p;hsa-miR-769-5p | 12 | EGFR | Sponge network | -3.056 | 0.02256 | 1.4 | 0.17026 | 0.275 |