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-139-5p | CASP1 | -0.7 | 0 | 1.75 | 0 | miRanda | -0.23 | 1.0E-5 | NA | |
2 | hsa-miR-361-5p | CASP1 | 0.05 | 0.38293 | 1.75 | 0 | miRanda | -0.32 | 0.01762 | NA | |
3 | hsa-miR-429 | CASP1 | -2.17 | 0 | 1.75 | 0 | miRanda | -0.33 | 0 | NA |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|
1 | CELL DEATH | 17 | 1001 | 2e-10 | 9.306e-07 |
2 | RESPONSE TO ENDOGENOUS STIMULUS | 16 | 1450 | 3.381e-07 | 0.0006429 |
3 | REGULATION OF CELL DEATH | 16 | 1472 | 4.145e-07 | 0.0006429 |
4 | CELLULAR RESPONSE TO ORGANIC SUBSTANCE | 17 | 1848 | 1.685e-06 | 0.00112 |
5 | RESPONSE TO OXYGEN CONTAINING COMPOUND | 15 | 1381 | 1.07e-06 | 0.00112 |
6 | RESPONSE TO EXTRACELLULAR STIMULUS | 9 | 441 | 1.52e-06 | 0.00112 |
7 | CELLULAR CHEMICAL HOMEOSTASIS | 10 | 570 | 1.458e-06 | 0.00112 |
8 | INTRINSIC APOPTOTIC SIGNALING PATHWAY | 6 | 152 | 2.371e-06 | 0.001379 |
9 | REGULATION OF CELLULAR COMPONENT BIOGENESIS | 11 | 767 | 2.877e-06 | 0.001487 |
10 | REGULATION OF PROTEIN LOCALIZATION | 12 | 950 | 3.513e-06 | 0.001635 |
11 | REGULATION OF PROTEIN COMPLEX ASSEMBLY | 8 | 375 | 4.465e-06 | 0.001889 |
12 | RESPONSE TO EXTERNAL STIMULUS | 16 | 1821 | 6.843e-06 | 0.001904 |
13 | AUTOPHAGY | 8 | 394 | 6.415e-06 | 0.001904 |
14 | REGULATION OF TRANSPORT | 16 | 1804 | 6.066e-06 | 0.001904 |
15 | NEURON DEATH | 4 | 47 | 6.168e-06 | 0.001904 |
16 | NEUROTROPHIN TRK RECEPTOR SIGNALING PATHWAY | 3 | 15 | 6.956e-06 | 0.001904 |
17 | CELLULAR HOMEOSTASIS | 10 | 676 | 6.645e-06 | 0.001904 |
18 | APOPTOTIC SIGNALING PATHWAY | 7 | 289 | 8.22e-06 | 0.002125 |
19 | POSITIVE REGULATION OF RESPONSE TO STIMULUS | 16 | 1929 | 1.425e-05 | 0.003385 |
20 | POSITIVE REGULATION OF PROTEIN METABOLIC PROCESS | 14 | 1492 | 1.455e-05 | 0.003385 |
21 | REGULATION OF HOMEOSTATIC PROCESS | 8 | 447 | 1.603e-05 | 0.003391 |
22 | RESPONSE TO ORGANIC CYCLIC COMPOUND | 11 | 917 | 1.565e-05 | 0.003391 |
23 | REGULATION OF VESICLE MEDIATED TRANSPORT | 8 | 462 | 2.032e-05 | 0.003783 |
24 | POSITIVE REGULATION OF CELL DEATH | 9 | 605 | 1.954e-05 | 0.003783 |
25 | POSITIVE REGULATION OF TRANSPORT | 11 | 936 | 1.894e-05 | 0.003783 |
26 | POSITIVE REGULATION OF CELLULAR COMPONENT ORGANIZATION | 12 | 1152 | 2.465e-05 | 0.004412 |
27 | POSITIVE REGULATION OF MOLECULAR FUNCTION | 15 | 1791 | 2.571e-05 | 0.00443 |
28 | NEUROTROPHIN SIGNALING PATHWAY | 3 | 23 | 2.669e-05 | 0.004435 |
29 | CELLULAR RESPONSE TO OXYGEN CONTAINING COMPOUND | 10 | 799 | 2.826e-05 | 0.004535 |
30 | RESPONSE TO OXIDATIVE STRESS | 7 | 352 | 2.932e-05 | 0.004548 |
31 | INTRINSIC APOPTOTIC SIGNALING PATHWAY IN RESPONSE TO DNA DAMAGE | 4 | 71 | 3.212e-05 | 0.004821 |
32 | NEUROGENESIS | 13 | 1402 | 3.598e-05 | 0.005231 |
33 | CELLULAR RESPONSE TO CARBOHYDRATE STIMULUS | 4 | 74 | 3.782e-05 | 0.005333 |
34 | POSITIVE REGULATION OF INTRACELLULAR TRANSPORT | 7 | 370 | 4.027e-05 | 0.005353 |
35 | CELLULAR GLUCOSE HOMEOSTASIS | 4 | 75 | 3.988e-05 | 0.005353 |
36 | POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION | 8 | 514 | 4.342e-05 | 0.005612 |
37 | RESPONSE TO STARVATION | 5 | 154 | 4.477e-05 | 0.005631 |
38 | ERBB SIGNALING PATHWAY | 4 | 79 | 4.893e-05 | 0.005991 |
39 | CHEMICAL HOMEOSTASIS | 10 | 874 | 6.036e-05 | 0.007157 |
40 | POSITIVE REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION | 10 | 876 | 6.153e-05 | 0.007157 |
41 | REGULATION OF CELLULAR LOCALIZATION | 12 | 1277 | 6.749e-05 | 0.007659 |
42 | RESPONSE TO HORMONE | 10 | 893 | 7.225e-05 | 0.008004 |
43 | REGULATION OF CATABOLIC PROCESS | 9 | 731 | 8.507e-05 | 0.009205 |
44 | POSITIVE REGULATION OF CELL COMMUNICATION | 13 | 1532 | 8.986e-05 | 0.009503 |
45 | NEURON APOPTOTIC PROCESS | 3 | 35 | 9.652e-05 | 0.009876 |
46 | REGULATION OF TRANSMEMBRANE TRANSPORT | 7 | 426 | 9.763e-05 | 0.009876 |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|
1 | PROTEIN DOMAIN SPECIFIC BINDING | 10 | 624 | 3.276e-06 | 0.003043 |
2 | PROTEIN C TERMINUS BINDING | 6 | 186 | 7.592e-06 | 0.003527 |
3 | ENZYME BINDING | 15 | 1737 | 1.788e-05 | 0.005537 |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|
1 | MITOCHONDRION | 17 | 1633 | 2.957e-07 | 0.0001727 |
2 | OUTER MEMBRANE | 6 | 190 | 8.574e-06 | 0.002504 |
3 | ENVELOPE | 12 | 1090 | 1.421e-05 | 0.002766 |
4 | VACUOLE | 12 | 1180 | 3.125e-05 | 0.003041 |
5 | LEADING EDGE MEMBRANE | 5 | 134 | 2.298e-05 | 0.003041 |
6 | CELL LEADING EDGE | 7 | 350 | 2.827e-05 | 0.003041 |
7 | MITOCHONDRIAL ENVELOPE | 9 | 691 | 5.521e-05 | 0.004606 |
8 | MITOCHONDRIAL PART | 10 | 953 | 0.0001238 | 0.009039 |
Num | Pathway | Pathview | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|---|
1 | AMPK_signaling_pathway_hsa04152 | 6 | 121 | 6.241e-07 | 3.245e-05 | |
2 | Apoptosis_hsa04210 | 5 | 138 | 2.647e-05 | 0.0006883 | |
3 | ErbB_signaling_pathway_hsa04012 | 4 | 85 | 6.52e-05 | 0.00113 | |
4 | Autophagy_animal_hsa04140 | 4 | 128 | 0.0003169 | 0.00412 | |
5 | Apelin_signaling_pathway_hsa04371 | 4 | 137 | 0.0004102 | 0.004267 | |
6 | mTOR_signaling_pathway_hsa04150 | 4 | 151 | 0.0005922 | 0.004534 | |
7 | Mitophagy_animal_hsa04137 | 3 | 65 | 0.0006104 | 0.004534 | |
8 | MAPK_signaling_pathway_hsa04010 | 5 | 295 | 0.0009101 | 0.005916 | |
9 | Focal_adhesion_hsa04510 | 4 | 199 | 0.001649 | 0.009528 | |
10 | Apoptosis_multiple_species_hsa04215 | 2 | 33 | 0.0032 | 0.01664 | |
11 | FoxO_signaling_pathway_hsa04068 | 3 | 132 | 0.004644 | 0.02196 | |
12 | Tight_junction_hsa04530 | 3 | 170 | 0.00932 | 0.03977 | |
13 | VEGF_signaling_pathway_hsa04370 | 2 | 59 | 0.009942 | 0.03977 | |
14 | PI3K_Akt_signaling_pathway_hsa04151 | 4 | 352 | 0.01231 | 0.04522 | |
15 | p53_signaling_pathway_hsa04115 | 2 | 68 | 0.01305 | 0.04522 | |
16 | cAMP_signaling_pathway_hsa04024 | 3 | 198 | 0.01405 | 0.04566 | |
17 | Rap1_signaling_pathway_hsa04015 | 3 | 206 | 0.01561 | 0.04774 | |
18 | Ras_signaling_pathway_hsa04014 | 3 | 232 | 0.02133 | 0.06161 | |
19 | HIF_1_signaling_pathway_hsa04066 | 2 | 100 | 0.02692 | 0.07368 | |
20 | Sphingolipid_signaling_pathway_hsa04071 | 2 | 118 | 0.03647 | 0.09483 | |
21 | Signaling_pathways_regulating_pluripotency_of_stem_cells_hsa04550 | 2 | 139 | 0.049 | 0.1209 | |
22 | Phospholipase_D_signaling_pathway_hsa04072 | 2 | 146 | 0.05348 | 0.1209 | |
23 | Wnt_signaling_pathway_hsa04310 | 2 | 146 | 0.05348 | 0.1209 | |
24 | Cellular_senescence_hsa04218 | 2 | 160 | 0.06285 | 0.1264 | |
25 | Jak_STAT_signaling_pathway_hsa04630 | 2 | 162 | 0.06423 | 0.1264 | |
26 | cGMP_PKG_signaling_pathway_hsa04022 | 2 | 163 | 0.06493 | 0.1264 | |
27 | Necroptosis_hsa04217 | 2 | 164 | 0.06563 | 0.1264 | |
28 | Regulation_of_actin_cytoskeleton_hsa04810 | 2 | 208 | 0.09859 | 0.1709 |