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.
miRNA-gene regulations
| 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-16-5p | SOCS5 | 0.75 | 0 | -0.44 | 4.0E-5 | miRNAWalker2 validate | -0.11 | 0.00049 | NA | |
| 2 | hsa-miR-342-3p | SOCS5 | -0.13 | 0.56103 | -0.44 | 4.0E-5 | miRanda | -0.15 | 0 | NA | |
| 3 | hsa-miR-590-5p | SOCS5 | 2.07 | 0 | -0.44 | 4.0E-5 | miRanda | -0.14 | 0 | NA | |
| 4 | hsa-miR-7-1-3p | SOCS5 | 2.61 | 0 | -0.44 | 4.0E-5 | mirMAP | -0.11 | 0 | NA |
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|
| 1 | PEPTIDYL TYROSINE AUTOPHOSPHORYLATION | 5 | 39 | 1.116e-09 | 5.191e-06 |
| 2 | REGULATION OF CELL ACTIVATION | 8 | 484 | 8.362e-08 | 5.694e-05 |
| 3 | INTRACELLULAR SIGNAL TRANSDUCTION | 12 | 1572 | 1.055e-07 | 5.694e-05 |
| 4 | ERBB SIGNALING PATHWAY | 5 | 79 | 4.224e-08 | 5.694e-05 |
| 5 | POSITIVE REGULATION OF CELL ACTIVATION | 7 | 311 | 7.769e-08 | 5.694e-05 |
| 6 | REGULATION OF IMMUNE SYSTEM PROCESS | 12 | 1403 | 2.988e-08 | 5.694e-05 |
| 7 | PEPTIDYL TYROSINE MODIFICATION | 6 | 186 | 9.125e-08 | 5.694e-05 |
| 8 | REGULATION OF HOMOTYPIC CELL CELL ADHESION | 7 | 307 | 7.112e-08 | 5.694e-05 |
| 9 | PROTEIN AUTOPHOSPHORYLATION | 6 | 192 | 1.101e-07 | 5.694e-05 |
| 10 | REGULATION OF CYTOKINE PRODUCTION | 8 | 563 | 2.659e-07 | 0.0001237 |
| 11 | REGULATION OF CELL CELL ADHESION | 7 | 380 | 3.027e-07 | 0.0001281 |
| 12 | POSITIVE REGULATION OF CELL CELL ADHESION | 6 | 243 | 4.414e-07 | 0.0001712 |
| 13 | NEGATIVE REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION | 7 | 437 | 7.751e-07 | 0.0002774 |
| 14 | DEFENSE RESPONSE | 10 | 1231 | 1.049e-06 | 0.0003487 |
| 15 | PHOSPHATE CONTAINING COMPOUND METABOLIC PROCESS | 12 | 1977 | 1.281e-06 | 0.0003973 |
| 16 | TRANSMEMBRANE RECEPTOR PROTEIN TYROSINE KINASE SIGNALING PATHWAY | 7 | 498 | 1.853e-06 | 0.000539 |
| 17 | LYMPHOCYTE COSTIMULATION | 4 | 78 | 2.544e-06 | 0.0006963 |
| 18 | NEGATIVE REGULATION OF MOLECULAR FUNCTION | 9 | 1079 | 3.489e-06 | 0.0009018 |
| 19 | NEGATIVE REGULATION OF TRANSFERASE ACTIVITY | 6 | 351 | 3.74e-06 | 0.000916 |
| 20 | REGULATION OF INNATE IMMUNE RESPONSE | 6 | 357 | 4.123e-06 | 0.0009593 |
| 21 | POSITIVE REGULATION OF CELL ADHESION | 6 | 376 | 5.553e-06 | 0.00123 |
| 22 | REGULATION OF IMMUNE RESPONSE | 8 | 858 | 6.262e-06 | 0.001325 |
| 23 | POSITIVE REGULATION OF IMMUNE SYSTEM PROCESS | 8 | 867 | 6.762e-06 | 0.001368 |
| 24 | REGULATION OF CELL ADHESION | 7 | 629 | 8.633e-06 | 0.001674 |
| 25 | NEGATIVE REGULATION OF KINASE ACTIVITY | 5 | 250 | 1.27e-05 | 0.002363 |
| 26 | NEGATIVE REGULATION OF PEPTIDYL TYROSINE PHOSPHORYLATION | 3 | 39 | 1.531e-05 | 0.002594 |
| 27 | ERBB2 SIGNALING PATHWAY | 3 | 39 | 1.531e-05 | 0.002594 |
| 28 | ENZYME LINKED RECEPTOR PROTEIN SIGNALING PATHWAY | 7 | 689 | 1.561e-05 | 0.002594 |
| 29 | RESPONSE TO CYTOKINE | 7 | 714 | 1.966e-05 | 0.003154 |
| 30 | NEGATIVE REGULATION OF RESPONSE TO STIMULUS | 9 | 1360 | 2.282e-05 | 0.003539 |
| 31 | REGULATION OF DEFENSE RESPONSE | 7 | 759 | 2.913e-05 | 0.004372 |
| 32 | REGULATION OF KINASE ACTIVITY | 7 | 776 | 3.357e-05 | 0.004881 |
| 33 | RESPONSE TO BACTERIUM | 6 | 528 | 3.8e-05 | 0.005358 |
| 34 | REGULATION OF RESPONSE TO STRESS | 9 | 1468 | 4.189e-05 | 0.005733 |
| 35 | EPIDERMAL GROWTH FACTOR RECEPTOR SIGNALING PATHWAY | 3 | 55 | 4.336e-05 | 0.005765 |
| 36 | INOSITOL PHOSPHATE METABOLIC PROCESS | 3 | 56 | 4.578e-05 | 0.005917 |
| 37 | REGULATION OF CELL PROLIFERATION | 9 | 1496 | 4.863e-05 | 0.006115 |
| 38 | PEPTIDYL AMINO ACID MODIFICATION | 7 | 841 | 5.605e-05 | 0.006864 |
| 39 | NEGATIVE REGULATION OF CELL COMMUNICATION | 8 | 1192 | 6.751e-05 | 0.008055 |
| 40 | IMMUNE SYSTEM PROCESS | 10 | 1984 | 7.271e-05 | 0.008458 |
| 41 | RESPONSE TO BIOTIC STIMULUS | 7 | 886 | 7.795e-05 | 0.008846 |
| 42 | CELLULAR RESPONSE TO CYTOKINE STIMULUS | 6 | 606 | 8.174e-05 | 0.009016 |
| 43 | PHOSPHORYLATION | 8 | 1228 | 8.332e-05 | 0.009016 |
| 44 | INNATE IMMUNE RESPONSE | 6 | 619 | 9.189e-05 | 0.009718 |
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|
| 1 | NON MEMBRANE SPANNING PROTEIN TYROSINE KINASE ACTIVITY | 5 | 46 | 2.641e-09 | 2.453e-06 |
| 2 | ADENYL NUCLEOTIDE BINDING | 11 | 1514 | 7.443e-07 | 0.0003457 |
| 3 | PROTEIN TYROSINE KINASE ACTIVITY | 5 | 176 | 2.296e-06 | 0.0007111 |
| 4 | KINASE BINDING | 7 | 606 | 6.766e-06 | 0.001006 |
| 5 | RIBONUCLEOTIDE BINDING | 11 | 1860 | 5.68e-06 | 0.001006 |
| 6 | PHOSPHOLIPASE C ACTIVITY | 3 | 31 | 7.578e-06 | 0.001006 |
| 7 | PHOSPHOLIPASE ACTIVITY | 4 | 94 | 5.366e-06 | 0.001006 |
| 8 | LIPASE ACTIVITY | 4 | 117 | 1.28e-05 | 0.001486 |
| 9 | PHOSPHOPROTEIN BINDING | 3 | 60 | 5.633e-05 | 0.005247 |
| 10 | KINASE ACTIVITY | 7 | 842 | 5.648e-05 | 0.005247 |
| 11 | PROTEIN KINASE ACTIVITY | 6 | 640 | 0.0001104 | 0.009325 |
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|
| 1 | EXTRINSIC COMPONENT OF CYTOPLASMIC SIDE OF PLASMA MEMBRANE | 5 | 98 | 1.253e-07 | 7.315e-05 |
| 2 | EXTRINSIC COMPONENT OF PLASMA MEMBRANE | 5 | 136 | 6.431e-07 | 0.0001878 |
| 3 | CYTOPLASMIC SIDE OF MEMBRANE | 5 | 170 | 1.937e-06 | 0.000377 |
| 4 | SIDE OF MEMBRANE | 6 | 428 | 1.163e-05 | 0.001541 |
| 5 | EXTRINSIC COMPONENT OF MEMBRANE | 5 | 252 | 1.32e-05 | 0.001541 |
Over-represented Pathway
| Num | Pathway | Pathview | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|---|
| 1 | hsa04630_Jak.STAT_signaling_pathway | 6 | 155 | 3.083e-08 | 5.55e-06 | |
| 2 | hsa04062_Chemokine_signaling_pathway | 5 | 189 | 3.257e-06 | 0.0002931 | |
| 3 | hsa04540_Gap_junction | 3 | 90 | 0.0001886 | 0.009547 | |
| 4 | hsa04912_GnRH_signaling_pathway | 3 | 101 | 0.0002652 | 0.009547 | |
| 5 | hsa04972_Pancreatic_secretion | 3 | 101 | 0.0002652 | 0.009547 | |
| 6 | hsa04380_Osteoclast_differentiation | 3 | 128 | 0.0005313 | 0.01594 | |
| 7 | hsa04020_Calcium_signaling_pathway | 3 | 177 | 0.001358 | 0.02748 | |
| 8 | hsa02010_ABC_transporters | 2 | 44 | 0.001374 | 0.02748 | |
| 9 | hsa04973_Carbohydrate_digestion_and_absorption | 2 | 44 | 0.001374 | 0.02748 | |
| 10 | hsa00562_Inositol_phosphate_metabolism | 2 | 57 | 0.002295 | 0.04132 | |
| 11 | hsa04720_Long.term_potentiation | 2 | 70 | 0.003439 | 0.045 | |
| 12 | hsa04730_Long.term_depression | 2 | 70 | 0.003439 | 0.045 | |
| 13 | hsa04520_Adherens_junction | 2 | 73 | 0.003734 | 0.045 | |
| 14 | hsa04971_Gastric_acid_secretion | 2 | 74 | 0.003834 | 0.045 | |
| 15 | hsa04662_B_cell_receptor_signaling_pathway | 2 | 75 | 0.003936 | 0.045 | |
| 16 | hsa04370_VEGF_signaling_pathway | 2 | 76 | 0.00404 | 0.045 | |
| 17 | hsa04070_Phosphatidylinositol_signaling_system | 2 | 78 | 0.00425 | 0.045 | |
| 18 | hsa04012_ErbB_signaling_pathway | 2 | 87 | 0.005258 | 0.05207 | |
| 19 | hsa04970_Salivary_secretion | 2 | 89 | 0.005496 | 0.05207 | |
| 20 | hsa04916_Melanogenesis | 2 | 101 | 0.007023 | 0.06321 | |
| 21 | hsa04660_T_cell_receptor_signaling_pathway | 2 | 108 | 0.007993 | 0.06851 | |
| 22 | hsa04270_Vascular_smooth_muscle_contraction | 2 | 116 | 0.00917 | 0.07503 | |
| 23 | hsa04722_Neurotrophin_signaling_pathway | 2 | 127 | 0.01091 | 0.08537 | |
| 24 | hsa04530_Tight_junction | 2 | 133 | 0.01191 | 0.08935 | |
| 25 | hsa04910_Insulin_signaling_pathway | 2 | 138 | 0.01278 | 0.09202 | |
| 26 | hsa04310_Wnt_signaling_pathway | 2 | 151 | 0.01516 | 0.105 | |
| 27 | hsa04510_Focal_adhesion | 2 | 200 | 0.02567 | 0.165 | |
| 28 | hsa04151_PI3K_AKT_signaling_pathway | 2 | 351 | 0.0707 | 0.4105 |
