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-107 | LMOD1 | 1.31 | 0 | -4.98 | 0 | miRanda | -1.65 | 0 | NA | |
| 2 | hsa-miR-182-5p | LMOD1 | 3.54 | 0 | -4.98 | 0 | miRNATAP | -0.79 | 0 | NA | |
| 3 | hsa-miR-26a-2-3p | LMOD1 | 0.82 | 0.00017 | -4.98 | 0 | mirMAP | -0.46 | 0.00028 | NA | |
| 4 | hsa-miR-324-5p | LMOD1 | 2.96 | 0 | -4.98 | 0 | PITA; miRanda | -0.99 | 0 | NA | |
| 5 | hsa-miR-326 | LMOD1 | 0.72 | 0.06103 | -4.98 | 0 | miRanda | -0.2 | 0.00487 | NA | |
| 6 | hsa-miR-330-5p | LMOD1 | 1.15 | 0 | -4.98 | 0 | miRanda | -1.03 | 0 | NA | |
| 7 | hsa-miR-335-5p | LMOD1 | 1.77 | 0 | -4.98 | 0 | miRNAWalker2 validate | -0.39 | 0 | NA | |
| 8 | hsa-miR-421 | LMOD1 | 1.18 | 1.0E-5 | -4.98 | 0 | miRanda | -0.8 | 0 | NA | |
| 9 | hsa-miR-429 | LMOD1 | 4.49 | 0 | -4.98 | 0 | miRNATAP | -0.47 | 0 | NA | |
| 10 | hsa-miR-96-5p | LMOD1 | 4.89 | 0 | -4.98 | 0 | TargetScan; miRNATAP | -0.76 | 0 | NA |
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|
| 1 | MRNA 3 END PROCESSING | 7 | 72 | 2.002e-10 | 9.318e-07 |
| 2 | MRNA PROCESSING | 11 | 432 | 1.699e-09 | 2.796e-06 |
| 3 | RNA 3 END PROCESSING | 7 | 98 | 1.803e-09 | 2.796e-06 |
| 4 | DNA REPLICATION INITIATION | 5 | 29 | 4.653e-09 | 4.331e-06 |
| 5 | RNA POLYADENYLATION | 5 | 29 | 4.653e-09 | 4.331e-06 |
| 6 | MITOTIC CELL CYCLE | 13 | 766 | 5.967e-09 | 4.628e-06 |
| 7 | MRNA METABOLIC PROCESS | 11 | 611 | 6.066e-08 | 4.032e-05 |
| 8 | DNA TEMPLATED TRANSCRIPTION TERMINATION | 6 | 101 | 8.626e-08 | 4.46e-05 |
| 9 | RNA SPLICING | 9 | 367 | 8.604e-08 | 4.46e-05 |
| 10 | RNA SPLICING VIA TRANSESTERIFICATION REACTIONS | 8 | 267 | 1.062e-07 | 4.943e-05 |
| 11 | RNA PROCESSING | 12 | 835 | 1.593e-07 | 5.701e-05 |
| 12 | CELL CYCLE G1 S PHASE TRANSITION | 6 | 111 | 1.516e-07 | 5.701e-05 |
| 13 | G1 S TRANSITION OF MITOTIC CELL CYCLE | 6 | 111 | 1.516e-07 | 5.701e-05 |
| 14 | TERMINATION OF RNA POLYMERASE II TRANSCRIPTION | 5 | 62 | 2.403e-07 | 7.987e-05 |
| 15 | POSITIVE REGULATION OF ORGANELLE ORGANIZATION | 10 | 573 | 3.554e-07 | 9.729e-05 |
| 16 | DNA REPLICATION | 7 | 208 | 3.289e-07 | 9.729e-05 |
| 17 | CELL CYCLE PROCESS | 13 | 1081 | 3.382e-07 | 9.729e-05 |
| 18 | CELL CYCLE | 14 | 1316 | 4.715e-07 | 0.0001219 |
| 19 | REGULATION OF RNA STABILITY | 6 | 139 | 5.745e-07 | 0.0001407 |
| 20 | REGULATION OF ORGANELLE ORGANIZATION | 13 | 1178 | 8.986e-07 | 0.0002091 |
| 21 | CELL CYCLE PHASE TRANSITION | 7 | 255 | 1.293e-06 | 0.0002864 |
| 22 | DNA DEPENDENT DNA REPLICATION | 5 | 99 | 2.501e-06 | 0.000529 |
| 23 | INNATE IMMUNE RESPONSE ACTIVATING CELL SURFACE RECEPTOR SIGNALING PATHWAY | 5 | 106 | 3.504e-06 | 0.0007088 |
| 24 | POSITIVE REGULATION OF LIGASE ACTIVITY | 5 | 110 | 4.204e-06 | 0.0007907 |
| 25 | POSITIVE REGULATION OF PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL | 6 | 196 | 4.248e-06 | 0.0007907 |
| 26 | DNA METABOLIC PROCESS | 10 | 758 | 4.44e-06 | 0.0007946 |
| 27 | FC RECEPTOR SIGNALING PATHWAY | 6 | 206 | 5.655e-06 | 0.0009746 |
| 28 | CHROMOSOME ORGANIZATION | 11 | 1009 | 8.428e-06 | 0.001401 |
| 29 | REGULATION OF LIGASE ACTIVITY | 5 | 130 | 9.518e-06 | 0.001527 |
| 30 | POSITIVE REGULATION OF GENE EXPRESSION | 14 | 1733 | 1.215e-05 | 0.001884 |
| 31 | MRNA CLEAVAGE | 3 | 21 | 1.285e-05 | 0.001929 |
| 32 | FC EPSILON RECEPTOR SIGNALING PATHWAY | 5 | 142 | 1.461e-05 | 0.002124 |
| 33 | T CELL RECEPTOR SIGNALING PATHWAY | 5 | 146 | 1.671e-05 | 0.002356 |
| 34 | POSITIVE REGULATION OF CHROMOSOME ORGANIZATION | 5 | 150 | 1.904e-05 | 0.002606 |
| 35 | ANAPHASE PROMOTING COMPLEX DEPENDENT CATABOLIC PROCESS | 4 | 77 | 2.453e-05 | 0.003261 |
| 36 | PROTEASOMAL PROTEIN CATABOLIC PROCESS | 6 | 271 | 2.683e-05 | 0.003468 |
| 37 | REGULATION OF CELLULAR PROTEIN CATABOLIC PROCESS | 6 | 274 | 2.854e-05 | 0.003589 |
| 38 | DNA GEOMETRIC CHANGE | 4 | 81 | 2.996e-05 | 0.003669 |
| 39 | REGULATION OF MRNA 3 END PROCESSING | 3 | 28 | 3.132e-05 | 0.003736 |
| 40 | REGULATION OF PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL | 6 | 280 | 3.222e-05 | 0.003749 |
| 41 | POSITIVE REGULATION OF CHROMATIN MODIFICATION | 4 | 85 | 3.623e-05 | 0.004112 |
| 42 | POSITIVE REGULATION OF DNA METABOLIC PROCESS | 5 | 185 | 5.2e-05 | 0.005761 |
| 43 | HISTONE UBIQUITINATION | 3 | 34 | 5.668e-05 | 0.006133 |
| 44 | POSITIVE REGULATION OF CELLULAR PROTEIN CATABOLIC PROCESS | 5 | 192 | 6.202e-05 | 0.006274 |
| 45 | NEGATIVE REGULATION OF MRNA METABOLIC PROCESS | 3 | 35 | 6.19e-05 | 0.006274 |
| 46 | PROTEIN UBIQUITINATION | 8 | 629 | 5.964e-05 | 0.006274 |
| 47 | ANTIGEN RECEPTOR MEDIATED SIGNALING PATHWAY | 5 | 195 | 6.675e-05 | 0.006471 |
| 48 | REGULATION OF MITOTIC CELL CYCLE | 7 | 468 | 6.654e-05 | 0.006471 |
| 49 | REGULATION OF CELL CYCLE PHASE TRANSITION | 6 | 321 | 6.889e-05 | 0.006542 |
| 50 | IMMUNE RESPONSE REGULATING CELL SURFACE RECEPTOR SIGNALING PATHWAY | 6 | 323 | 7.13e-05 | 0.006635 |
| 51 | REGULATION OF PROTEIN UBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS | 4 | 103 | 7.687e-05 | 0.007013 |
| 52 | ACTIVATION OF INNATE IMMUNE RESPONSE | 5 | 204 | 8.262e-05 | 0.007393 |
| 53 | POSITIVE REGULATION OF BIOSYNTHETIC PROCESS | 13 | 1805 | 9.065e-05 | 0.007958 |
| 54 | REGULATION OF DNA METABOLIC PROCESS | 6 | 340 | 9.456e-05 | 0.008148 |
| 55 | CELLULAR RESPONSE TO STRESS | 12 | 1565 | 0.0001006 | 0.008507 |
| 56 | WNT SIGNALING PATHWAY | 6 | 351 | 0.0001126 | 0.00919 |
| 57 | NEGATIVE REGULATION OF TRANSFERASE ACTIVITY | 6 | 351 | 0.0001126 | 0.00919 |
| 58 | REGULATION OF CELLULAR RESPONSE TO STRESS | 8 | 691 | 0.0001148 | 0.009213 |
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|
| 1 | POLY A RNA BINDING | 15 | 1170 | 1.356e-08 | 8.031e-06 |
| 2 | RNA BINDING | 17 | 1598 | 1.729e-08 | 8.031e-06 |
| 3 | MRNA BINDING | 6 | 155 | 1.088e-06 | 0.000337 |
| 4 | DNA HELICASE ACTIVITY | 4 | 53 | 5.515e-06 | 0.001281 |
| 5 | THREONINE TYPE PEPTIDASE ACTIVITY | 3 | 21 | 1.285e-05 | 0.002388 |
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|
| 1 | NUCLEOPLASM PART | 13 | 708 | 2.317e-09 | 1.353e-06 |
| 2 | MCM COMPLEX | 4 | 11 | 6.647e-09 | 1.941e-06 |
| 3 | NUCLEAR CHROMOSOME TELOMERIC REGION | 5 | 132 | 1.025e-05 | 0.001289 |
| 4 | NUCLEAR BODY | 7 | 349 | 1.02e-05 | 0.001289 |
| 5 | PROTEASOME CORE COMPLEX | 3 | 20 | 1.103e-05 | 0.001289 |
| 6 | TRANSFERASE COMPLEX | 9 | 703 | 1.83e-05 | 0.001526 |
| 7 | HISTONE METHYLTRANSFERASE COMPLEX | 4 | 71 | 1.778e-05 | 0.001526 |
| 8 | PROTEASOME COMPLEX | 4 | 76 | 2.329e-05 | 0.0017 |
| 9 | CHROMOSOME TELOMERIC REGION | 5 | 162 | 2.758e-05 | 0.001789 |
| 10 | CHROMATIN | 7 | 441 | 4.575e-05 | 0.002429 |
| 11 | METHYLTRANSFERASE COMPLEX | 4 | 90 | 4.536e-05 | 0.002429 |
| 12 | MICROTUBULE ORGANIZING CENTER | 8 | 623 | 5.575e-05 | 0.002713 |
| 13 | NUCLEAR SPECK | 5 | 194 | 6.515e-05 | 0.002927 |
| 14 | MICROTUBULE CYTOSKELETON | 10 | 1068 | 8.504e-05 | 0.003116 |
| 15 | CHROMOSOMAL REGION | 6 | 330 | 8.024e-05 | 0.003116 |
| 16 | CENTROSOME | 7 | 487 | 8.538e-05 | 0.003116 |
| 17 | CHROMOSOME | 9 | 880 | 0.0001049 | 0.003604 |
| 18 | NUCLEAR CHROMOSOME | 7 | 523 | 0.000133 | 0.004316 |
| 19 | RNA POLYMERASE COMPLEX | 4 | 122 | 0.0001481 | 0.004495 |
| 20 | RIBONUCLEOPROTEIN COMPLEX | 8 | 721 | 0.0001539 | 0.004495 |
Over-represented Pathway
| Num | Pathway | Pathview | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|---|
| 1 | Cell_cycle_hsa04110 | 8 | 124 | 2.555e-10 | 1.329e-08 | |
| 2 | ErbB_signaling_pathway_hsa04012 | 2 | 85 | 0.01504 | 0.3911 | |
| 3 | FoxO_signaling_pathway_hsa04068 | 2 | 132 | 0.03414 | 0.4531 | |
| 4 | Signaling_pathways_regulating_pluripotency_of_stem_cells_hsa04550 | 2 | 139 | 0.03751 | 0.4531 | |
| 5 | mTOR_signaling_pathway_hsa04150 | 2 | 151 | 0.04357 | 0.4531 | |
| 6 | Focal_adhesion_hsa04510 | 2 | 199 | 0.07099 | 0.5692 | |
| 7 | Regulation_of_actin_cytoskeleton_hsa04810 | 2 | 208 | 0.07663 | 0.5692 | |
| 8 | Endocytosis_hsa04144 | 2 | 244 | 0.1005 | 0.5806 | |
| 9 | PI3K_Akt_signaling_pathway_hsa04151 | 2 | 352 | 0.1812 | 0.6263 |
