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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

(Download full result)

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-28-5p ACVRL1 -0.43 0 0.73 0 miRanda; mirMAP -0.3 0 NA
2 hsa-miR-590-5p ACVRL1 -0.1 0.31003 0.73 0 mirMAP -0.28 0 NA
3 hsa-miR-32-3p BMP2 0.22 0.20722 -0.18 0.35911 mirMAP -0.14 0.01775 NA
4 hsa-miR-139-5p TGFB1 -2.11 0 0.08 0.68861 miRanda -0.17 0.00036 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 REGULATION OF CARTILAGE DEVELOPMENT 3 63 2.979e-08 4.62e-05
2 REGULATION OF PATHWAY RESTRICTED SMAD PROTEIN PHOSPHORYLATION 3 60 2.567e-08 4.62e-05
3 POSITIVE REGULATION OF PATHWAY RESTRICTED SMAD PROTEIN PHOSPHORYLATION 3 48 1.297e-08 4.62e-05
4 POSITIVE REGULATION OF TRANSMEMBRANE RECEPTOR PROTEIN SERINE THREONINE KINASE SIGNALING PATHWAY 3 100 1.213e-07 0.0001411
5 POSITIVE REGULATION OF EPITHELIAL CELL PROLIFERATION 3 154 4.477e-07 0.0004167
6 TRANSMEMBRANE RECEPTOR PROTEIN SERINE THREONINE KINASE SIGNALING PATHWAY 3 190 8.44e-07 0.0006545
7 PATHWAY RESTRICTED SMAD PROTEIN PHOSPHORYLATION 2 13 1.17e-06 0.0006803
8 REGULATION OF TRANSMEMBRANE RECEPTOR PROTEIN SERINE THREONINE KINASE SIGNALING PATHWAY 3 207 1.093e-06 0.0006803
9 NEGATIVE REGULATION OF CELL ADHESION 3 223 1.368e-06 0.0007072
10 REGULATION OF CARDIAC MUSCLE CELL DIFFERENTIATION 2 19 2.564e-06 0.001193
11 REGULATION OF EPITHELIAL CELL PROLIFERATION 3 285 2.864e-06 0.001211
12 NEGATIVE REGULATION OF BLOOD VESSEL ENDOTHELIAL CELL MIGRATION 2 24 4.137e-06 0.001387
13 REGULATION OF ODONTOGENESIS 2 24 4.137e-06 0.001387
14 TUBE MORPHOGENESIS 3 323 4.174e-06 0.001387
15 REGULATION OF HEART MORPHOGENESIS 2 29 6.085e-06 0.00177
16 POSITIVE REGULATION OF CARTILAGE DEVELOPMENT 2 29 6.085e-06 0.00177
17 POSITIVE REGULATION OF EPITHELIAL TO MESENCHYMAL TRANSITION 2 34 8.406e-06 0.002173
18 MORPHOGENESIS OF AN EPITHELIUM 3 400 7.941e-06 0.002173
19 NEGATIVE REGULATION OF MUSCLE ORGAN DEVELOPMENT 2 36 9.44e-06 0.002196
20 NEGATIVE REGULATION OF MUSCLE TISSUE DEVELOPMENT 2 36 9.44e-06 0.002196
21 ANATOMICAL STRUCTURE MATURATION 2 39 1.11e-05 0.002246
22 POSITIVE REGULATION OF BIOMINERAL TISSUE DEVELOPMENT 2 38 1.053e-05 0.002246
23 NEGATIVE REGULATION OF ENDOTHELIAL CELL MIGRATION 2 39 1.11e-05 0.002246
24 RESPONSE TO GROWTH FACTOR 3 475 1.331e-05 0.002581
25 SENSORY ORGAN DEVELOPMENT 3 493 1.489e-05 0.002697
26 EPITHELIAL CELL DIFFERENTIATION 3 495 1.507e-05 0.002697
27 POSITIVE REGULATION OF DEPHOSPHORYLATION 2 47 1.619e-05 0.00279
28 REGULATION OF CARDIAC MUSCLE TISSUE DEVELOPMENT 2 48 1.689e-05 0.002808
29 TISSUE MORPHOGENESIS 3 533 1.882e-05 0.002866
30 POSITIVE REGULATION OF STEM CELL DIFFERENTIATION 2 50 1.835e-05 0.002866
31 REGULATION OF BLOOD VESSEL ENDOTHELIAL CELL MIGRATION 2 51 1.909e-05 0.002866
32 NEGATIVE REGULATION OF EPITHELIAL CELL MIGRATION 2 53 2.064e-05 0.002949
33 TUBE DEVELOPMENT 3 552 2.091e-05 0.002949
34 SMAD PROTEIN SIGNAL TRANSDUCTION 2 56 2.306e-05 0.00298
35 NEGATIVE REGULATION OF MUSCLE CELL DIFFERENTIATION 2 55 2.224e-05 0.00298
36 EPITHELIAL TO MESENCHYMAL TRANSITION 2 56 2.306e-05 0.00298
37 CHONDROCYTE DIFFERENTIATION 2 60 2.65e-05 0.003333
38 NEGATIVE REGULATION OF CELL DIFFERENTIATION 3 609 2.81e-05 0.003441
39 REGULATION OF CELL ADHESION 3 629 3.096e-05 0.003694
40 REGULATION OF EPITHELIAL TO MESENCHYMAL TRANSITION 2 67 3.309e-05 0.003756
41 NEGATIVE REGULATION OF CELL PROLIFERATION 3 643 3.308e-05 0.003756
42 POSITIVE REGULATION OF ENDOTHELIAL CELL PROLIFERATION 2 68 3.41e-05 0.003777
43 CELL PROLIFERATION 3 672 3.777e-05 0.004087
44 REGULATION OF BIOMINERAL TISSUE DEVELOPMENT 2 75 4.153e-05 0.004294
45 ENZYME LINKED RECEPTOR PROTEIN SIGNALING PATHWAY 3 689 4.071e-05 0.004294
46 POSITIVE REGULATION OF OSSIFICATION 2 84 5.215e-05 0.005275
47 REGULATION OF STRIATED MUSCLE CELL DIFFERENTIATION 2 85 5.34e-05 0.005287
48 TISSUE REMODELING 2 87 5.596e-05 0.00542
49 REGULATION OF CELLULAR COMPONENT MOVEMENT 3 771 5.708e-05 0.00542
50 MESONEPHROS DEVELOPMENT 2 90 5.99e-05 0.005574
51 POSITIVE REGULATION OF CELL PROLIFERATION 3 814 6.718e-05 0.005684
52 TRANSFORMING GROWTH FACTOR BETA RECEPTOR SIGNALING PATHWAY 2 95 6.677e-05 0.005684
53 RESPONSE TO BMP 2 94 6.537e-05 0.005684
54 NEGATIVE REGULATION OF DEVELOPMENTAL PROCESS 3 801 6.401e-05 0.005684
55 CELLULAR RESPONSE TO BMP STIMULUS 2 94 6.537e-05 0.005684
56 POSITIVE REGULATION OF CELL DIFFERENTIATION 3 823 6.944e-05 0.005769
57 REGULATION OF ENDOTHELIAL CELL PROLIFERATION 2 98 7.107e-05 0.005802
58 REGULATION OF MUSCLE TISSUE DEVELOPMENT 2 103 7.853e-05 0.006194
59 REGULATION OF MUSCLE ORGAN DEVELOPMENT 2 103 7.853e-05 0.006194
60 REGULATION OF FAT CELL DIFFERENTIATION 2 106 8.319e-05 0.006451
61 NEGATIVE REGULATION OF DNA METABOLIC PROCESS 2 111 9.125e-05 0.00696
62 REGULATION OF ENDOTHELIAL CELL MIGRATION 2 114 9.626e-05 0.006998
63 NOTCH SIGNALING PATHWAY 2 114 9.626e-05 0.006998
64 REGULATION OF STEM CELL DIFFERENTIATION 2 113 9.457e-05 0.006998
65 NEGATIVE REGULATION OF EPITHELIAL CELL PROLIFERATION 2 115 9.796e-05 0.007012
66 EPITHELIUM DEVELOPMENT 3 945 0.0001052 0.007304
67 PROTEIN PHOSPHORYLATION 3 944 0.0001048 0.007304
68 KIDNEY EPITHELIUM DEVELOPMENT 2 125 0.0001158 0.007922
69 POSITIVE REGULATION OF BINDING 2 127 0.0001195 0.007945
70 NEGATIVE REGULATION OF MULTICELLULAR ORGANISMAL PROCESS 3 983 0.0001184 0.007945
71 CELLULAR RESPONSE TO ENDOGENOUS STIMULUS 3 1008 0.0001277 0.008137
72 POSITIVE REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 3 1004 0.0001261 0.008137
73 BRANCHING MORPHOGENESIS OF AN EPITHELIAL TUBE 2 131 0.0001272 0.008137
74 MESENCHYMAL CELL DIFFERENTIATION 2 134 0.0001331 0.008256
75 REGULATION OF ANATOMICAL STRUCTURE MORPHOGENESIS 3 1021 0.0001327 0.008256
76 POSITIVE REGULATION OF PHOSPHATE METABOLIC PROCESS 3 1036 0.0001386 0.008376
77 POSITIVE REGULATION OF PHOSPHORUS METABOLIC PROCESS 3 1036 0.0001386 0.008376
78 NEGATIVE REGULATION OF CELL CELL ADHESION 2 138 0.0001412 0.008421
79 RESPONSE TO TRANSFORMING GROWTH FACTOR BETA 2 144 0.0001537 0.009054
80 CARTILAGE DEVELOPMENT 2 147 0.0001602 0.009317
81 REGULATION OF MUSCLE CELL DIFFERENTIATION 2 152 0.0001713 0.00984
NumGOOverlapSizeP ValueAdj. P Value
NumGOOverlapSizeP ValueAdj. P Value

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 TGF_beta_signaling_pathway_hsa04350 2 84 5.215e-05 0.002712
2 Hippo_signaling_pathway_hsa04390 2 154 0.0001758 0.004572
3 Cytokine_cytokine_receptor_interaction_hsa04060 2 270 0.0005399 0.009358

Quest ID: a23bd55a56ed3ecad6cb9c3e3d0ae3c8