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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-324-3p FGA 0.26 0.05061 -2.01 0 PITA -0.64 0 NA
2 hsa-miR-335-3p FGA -0.28 0.10663 -2.01 0 MirTarget -0.41 0 NA
3 hsa-miR-338-3p FGG 0.54 0.00461 -2.04 0 miRanda -0.29 0.00037 NA
4 hsa-miR-421 FGG 0.94 0 -2.04 0 miRanda -0.45 0 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 WOUND HEALING 9 470 1.336e-08 3.108e-05
2 EXTRACELLULAR STRUCTURE ORGANIZATION 8 304 8.453e-09 3.108e-05
3 FIBRINOLYSIS 4 21 2.097e-08 3.252e-05
4 RESPONSE TO WOUNDING 9 563 6.308e-08 7.338e-05
5 HEMOSTASIS 7 311 2.391e-07 0.0002225
6 PLATELET DEGRANULATION 5 107 4.277e-07 0.0003317
7 NEGATIVE REGULATION OF COAGULATION 4 48 6.636e-07 0.0004411
8 NEGATIVE REGULATION OF WOUND HEALING 4 58 1.432e-06 0.0008331
9 PLATELET ACTIVATION 5 142 1.74e-06 0.0008998
10 LOCOMOTION 10 1114 2.09e-06 0.0009261
11 REGULATION OF CELL ADHESION 8 629 2.189e-06 0.0009261
12 SINGLE ORGANISM CELL ADHESION 7 459 3.228e-06 0.0009758
13 POSITIVE REGULATION OF MAPK CASCADE 7 470 3.774e-06 0.0009758
14 REGULATION OF VESICLE MEDIATED TRANSPORT 7 462 3.37e-06 0.0009758
15 CELL SUBSTRATE ADHESION 5 164 3.532e-06 0.0009758
16 RESPONSE TO ORGANIC CYCLIC COMPOUND 9 917 3.761e-06 0.0009758
17 POSITIVE REGULATION OF PROTEIN METABOLIC PROCESS 11 1492 3.775e-06 0.0009758
18 REGULATION OF BINDING 6 283 2.75e-06 0.0009758
19 RESPONSE TO GROWTH FACTOR 7 475 4.046e-06 0.0009909
20 REGULATION OF CELL SUBSTRATE ADHESION 5 173 4.587e-06 0.001067
21 REGULATION OF BODY FLUID LEVELS 7 506 6.128e-06 0.001296
22 RESPONSE TO KETONE 5 182 5.875e-06 0.001296
23 CELL MORPHOGENESIS INVOLVED IN DIFFERENTIATION 7 513 6.704e-06 0.0013
24 NEGATIVE REGULATION OF MULTICELLULAR ORGANISMAL PROCESS 9 983 6.628e-06 0.0013
25 TRANSMEMBRANE RECEPTOR PROTEIN SERINE THREONINE KINASE SIGNALING PATHWAY 5 190 7.243e-06 0.001348
26 REGULATION OF COAGULATION 4 88 7.64e-06 0.001367
27 RESPONSE TO BACTERIUM 7 528 8.093e-06 0.001395
28 POSITIVE REGULATION OF PHOSPHATE METABOLIC PROCESS 9 1036 1.014e-05 0.001506
29 POSITIVE REGULATION OF PHOSPHORUS METABOLIC PROCESS 9 1036 1.014e-05 0.001506
30 TRANSFORMING GROWTH FACTOR BETA RECEPTOR SIGNALING PATHWAY 4 95 1.036e-05 0.001506
31 MULTICELLULAR ORGANISM REPRODUCTION 8 768 9.546e-06 0.001506
32 BIOLOGICAL ADHESION 9 1032 9.827e-06 0.001506
33 CELL ACTIVATION 7 568 1.301e-05 0.001682
34 REGULATION OF PEPTIDYL TYROSINE PHOSPHORYLATION 5 213 1.261e-05 0.001682
35 POSITIVE REGULATION OF PROTEIN SECRETION 5 211 1.204e-05 0.001682
36 POSITIVE REGULATION OF SECRETION 6 370 1.276e-05 0.001682
37 POSITIVE REGULATION OF CELL ADHESION 6 376 1.398e-05 0.001736
38 RESPONSE TO OXYGEN CONTAINING COMPOUND 10 1381 1.418e-05 0.001736
39 RESPONSE TO FLUID SHEAR STRESS 3 34 1.591e-05 0.00187
40 REGULATED EXOCYTOSIS 5 224 1.607e-05 0.00187
41 CELL CELL ADHESION 7 608 2.02e-05 0.002292
42 POSITIVE REGULATION OF PROTEIN MODIFICATION PROCESS 9 1135 2.107e-05 0.002335
43 PLATELET AGGREGATION 3 39 2.419e-05 0.002617
44 CELL MATRIX ADHESION 4 119 2.522e-05 0.002631
45 RESPONSE TO EXTERNAL STIMULUS 11 1821 2.544e-05 0.002631
46 RESPONSE TO LIPID 8 888 2.732e-05 0.002763
47 REGULATION OF WOUND HEALING 4 126 3.157e-05 0.003125
48 REGULATION OF MAPK CASCADE 7 660 3.418e-05 0.003314
49 SKELETAL SYSTEM DEVELOPMENT 6 455 4.085e-05 0.003849
50 VESICLE MEDIATED TRANSPORT 9 1239 4.218e-05 0.003849
51 CELL GROWTH 4 135 4.136e-05 0.003849
52 CELLULAR RESPONSE TO ORGANIC CYCLIC COMPOUND 6 465 4.612e-05 0.004049
53 TAXIS 6 464 4.557e-05 0.004049
54 REGULATION OF SECRETION 7 699 4.926e-05 0.004216
55 RESPONSE TO TRANSFORMING GROWTH FACTOR BETA 4 144 5.322e-05 0.004216
56 REGULATION OF CELLULAR LOCALIZATION 9 1277 5.346e-05 0.004216
57 FACE DEVELOPMENT 3 50 5.132e-05 0.004216
58 MOVEMENT OF CELL OR SUBCELLULAR COMPONENT 9 1275 5.281e-05 0.004216
59 RESPONSE TO PROGESTERONE 3 50 5.132e-05 0.004216
60 HOMOTYPIC CELL CELL ADHESION 3 51 5.447e-05 0.004224
61 REGULATION OF PHOSPHORUS METABOLIC PROCESS 10 1618 5.588e-05 0.004262
62 CARTILAGE DEVELOPMENT 4 147 5.767e-05 0.004328
63 REPRODUCTION 9 1297 6.037e-05 0.004459
64 NEGATIVE REGULATION OF CELL DEVELOPMENT 5 303 6.804e-05 0.00487
65 REGULATION OF EXTRINSIC APOPTOTIC SIGNALING PATHWAY 4 153 6.738e-05 0.00487
66 NEGATIVE REGULATION OF RESPONSE TO WOUNDING 4 156 7.266e-05 0.005123
67 EXOCYTOSIS 5 310 7.579e-05 0.005264
68 POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION 6 514 8.036e-05 0.005499
69 CELLULAR RESPONSE TO BIOTIC STIMULUS 4 163 8.615e-05 0.005621
70 NEGATIVE REGULATION OF RESPONSE TO STIMULUS 9 1360 8.728e-05 0.005621
71 REGULATION OF PROTEIN MODIFICATION PROCESS 10 1710 8.939e-05 0.005621
72 RESPONSE TO MOLECULE OF BACTERIAL ORIGIN 5 321 8.934e-05 0.005621
73 VASCULAR PROCESS IN CIRCULATORY SYSTEM 4 163 8.615e-05 0.005621
74 POSITIVE REGULATION OF CELL MORPHOGENESIS INVOLVED IN DIFFERENTIATION 4 162 8.412e-05 0.005621
75 REGULATION OF CELLULAR COMPONENT MOVEMENT 7 771 9.141e-05 0.005671
76 POSITIVE REGULATION OF ERK1 AND ERK2 CASCADE 4 172 0.0001061 0.006415
77 DEVELOPMENTAL GROWTH 5 333 0.0001062 0.006415
78 CELLULAR RESPONSE TO OXYGEN CONTAINING COMPOUND 7 799 0.0001143 0.006816
79 REGULATION OF MACROPHAGE CYTOKINE PRODUCTION 2 12 0.0001328 0.007821
80 RESPONSE TO ENDOGENOUS STIMULUS 9 1450 0.0001429 0.008012
81 CELL JUNCTION ORGANIZATION 4 185 0.0001405 0.008012
82 REGULATION OF CELLULAR AMIDE METABOLIC PROCESS 5 354 0.0001414 0.008012
83 REGULATION OF TRANSPORT 10 1804 0.0001401 0.008012
84 IMMUNE SYSTEM DEVELOPMENT 6 582 0.0001588 0.008232
85 PATHWAY RESTRICTED SMAD PROTEIN PHOSPHORYLATION 2 13 0.0001568 0.008232
86 LEUKOCYTE TETHERING OR ROLLING 2 13 0.0001568 0.008232
87 REGULATION OF PLASMA MEMBRANE ORGANIZATION 3 73 0.0001592 0.008232
88 LEUKOCYTE ADHESION TO VASCULAR ENDOTHELIAL CELL 2 13 0.0001568 0.008232
89 REGULATION OF CELL DEVELOPMENT 7 836 0.0001514 0.008232
90 REGULATION OF APOPTOTIC SIGNALING PATHWAY 5 363 0.000159 0.008232
91 CONNECTIVE TISSUE DEVELOPMENT 4 194 0.0001686 0.00862
92 POSITIVE REGULATION OF CELLULAR COMPONENT ORGANIZATION 8 1152 0.0001711 0.008653
93 STRESS FIBER ASSEMBLY 2 14 0.0001828 0.008951
94 CONTRACTILE ACTIN FILAMENT BUNDLE ASSEMBLY 2 14 0.0001828 0.008951
95 REGULATION OF EXTRACELLULAR MATRIX DISASSEMBLY 2 14 0.0001828 0.008951
96 NEGATIVE REGULATION OF APOPTOTIC SIGNALING PATHWAY 4 200 0.0001895 0.009183
97 REGULATION OF CELL CELL ADHESION 5 380 0.0001967 0.009435
98 POSITIVE REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION 7 876 0.0002021 0.009597
NumGOOverlapSizeP ValueAdj. P Value
1 RECEPTOR BINDING 11 1476 3.399e-06 0.003157
NumGOOverlapSizeP ValueAdj. P Value
1 PLATELET ALPHA GRANULE LUMEN 5 55 1.474e-08 8.61e-06
2 PLATELET ALPHA GRANULE 5 75 7.169e-08 2.093e-05
3 SECRETORY GRANULE LUMEN 5 85 1.349e-07 2.626e-05
4 VESICLE LUMEN 5 106 4.081e-07 5.958e-05
5 SECRETORY GRANULE 6 352 9.609e-06 0.001122
6 SECRETORY VESICLE 6 461 4.395e-05 0.004278
7 MEMBRANE MICRODOMAIN 5 288 5.349e-05 0.004463
8 CELL SURFACE 7 757 8.148e-05 0.005948
9 ROUGH ENDOPLASMIC RETICULUM 3 71 0.0001466 0.008562
10 INVADOPODIUM 2 12 0.0001328 0.008562

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 Focal_adhesion_hsa04510 4 199 0.0001859 0.003137
2 Rap1_signaling_pathway_hsa04015 4 206 0.0002122 0.003137
3 Regulation_of_actin_cytoskeleton_hsa04810 4 208 0.0002201 0.003137
4 TGF_beta_signaling_pathway_hsa04350 3 84 0.0002413 0.003137
5 FoxO_signaling_pathway_hsa04068 3 132 0.0009057 0.009419
6 Cellular_senescence_hsa04218 3 160 0.001576 0.01366
7 VEGF_signaling_pathway_hsa04370 2 59 0.0033 0.02451
8 Adherens_junction_hsa04520 2 72 0.004873 0.03167
9 ECM_receptor_interaction_hsa04512 2 82 0.006275 0.03401
10 ErbB_signaling_pathway_hsa04012 2 85 0.006727 0.03401
11 Gap_junction_hsa04540 2 88 0.007194 0.03401
12 MAPK_signaling_pathway_hsa04010 3 295 0.008741 0.03788
13 Cell_cycle_hsa04110 2 124 0.01388 0.05229
14 PI3K_Akt_signaling_pathway_hsa04151 3 352 0.01408 0.05229
15 Cell_adhesion_molecules_.CAMs._hsa04514 2 145 0.01865 0.06139
16 Phospholipase_D_signaling_pathway_hsa04072 2 146 0.01889 0.06139
17 Hippo_signaling_pathway_hsa04390 2 154 0.02087 0.06385
18 Tight_junction_hsa04530 2 170 0.02509 0.07249
19 Ras_signaling_pathway_hsa04014 2 232 0.0443 0.1213
20 Cytokine_cytokine_receptor_interaction_hsa04060 2 270 0.05806 0.151

Quest ID: 0323011a5f0893c238f970c5ea213120