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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-132-3p EIF4A2 0.32 0.00272 0.03 0.737 miRNATAP -0.17 5.0E-5 NA
2 hsa-miR-342-3p EIF4A2 -0.32 0.04498 0.03 0.737 miRanda -0.12 1.0E-5 NA
3 hsa-miR-484 EIF4A2 0.09 0.45398 0.03 0.737 miRNATAP -0.12 0.00201 NA
NumGOOverlapSizeP ValueAdj. P Value
1 ORGANONITROGEN COMPOUND METABOLIC PROCESS 44 1796 2.099e-14 9.767e-11
2 AMIDE BIOSYNTHETIC PROCESS 23 507 6.249e-13 1.454e-09
3 ORGANONITROGEN COMPOUND BIOSYNTHETIC PROCESS 31 1024 1.787e-12 2.771e-09
4 PEPTIDE METABOLIC PROCESS 23 571 7.126e-12 8.29e-09
5 POSTTRANSCRIPTIONAL REGULATION OF GENE EXPRESSION 20 448 3.092e-11 2.877e-08
6 ORGANOPHOSPHATE METABOLIC PROCESS 26 885 2.826e-10 2.192e-07
7 SINGLE ORGANISM BIOSYNTHETIC PROCESS 32 1340 3.469e-10 2.306e-07
8 NUCLEOBASE CONTAINING SMALL MOLECULE METABOLIC PROCESS 20 535 7.044e-10 3.642e-07
9 NCRNA METABOLIC PROCESS 20 533 6.601e-10 3.642e-07
10 CELLULAR AMIDE METABOLIC PROCESS 23 727 8.463e-10 3.938e-07
11 PHOSPHATE CONTAINING COMPOUND METABOLIC PROCESS 37 1977 9.215e-09 3.573e-06
12 RIBONUCLEOPROTEIN COMPLEX BIOGENESIS 17 440 9.136e-09 3.573e-06
13 NUCLEOSIDE MONOPHOSPHATE METABOLIC PROCESS 13 239 1.055e-08 3.775e-06
14 REGULATION OF CELLULAR AMIDE METABOLIC PROCESS 15 354 2.148e-08 7.14e-06
15 NUCLEOSIDE TRIPHOSPHATE METABOLIC PROCESS 12 228 5.724e-08 1.776e-05
16 NCRNA PROCESSING 15 386 6.706e-08 1.95e-05
17 PURINE CONTAINING COMPOUND METABOLIC PROCESS 14 394 5.55e-07 0.0001519
18 TRANSLATIONAL ELONGATION 8 111 9.633e-07 0.000249
19 TRNA AMINOACYLATION 6 52 1.454e-06 0.0002977
20 AMINO ACID ACTIVATION 6 52 1.454e-06 0.0002977
21 RIBOSOME BIOGENESIS 12 308 1.436e-06 0.0002977
22 RRNA METABOLIC PROCESS 11 255 1.501e-06 0.0002977
23 GLYCOSYL COMPOUND METABOLIC PROCESS 13 368 1.535e-06 0.0002977
24 REGULATION OF TRANSLATIONAL INITIATION 7 82 1.504e-06 0.0002977
25 MONOSACCHARIDE BIOSYNTHETIC PROCESS 6 54 1.825e-06 0.0003396
26 TRNA METABOLIC PROCESS 9 176 3.519e-06 0.0006298
27 NADH METABOLIC PROCESS 5 35 3.857e-06 0.0006647
28 RNA PROCESSING 19 835 4.282e-06 0.0007115
29 GENERATION OF PRECURSOR METABOLITES AND ENERGY 11 292 5.53e-06 0.0008872
30 MITOCHONDRIAL TRANSLATION 7 107 8.947e-06 0.001301
31 INNATE IMMUNE RESPONSE ACTIVATING CELL SURFACE RECEPTOR SIGNALING PATHWAY 7 106 8.41e-06 0.001301
32 OXIDOREDUCTION COENZYME METABOLIC PROCESS 7 107 8.947e-06 0.001301
33 FC RECEPTOR SIGNALING PATHWAY 9 206 1.259e-05 0.001775
34 DNA BIOSYNTHETIC PROCESS 7 121 2.001e-05 0.002739
35 SMALL MOLECULE METABOLIC PROCESS 28 1767 2.134e-05 0.002837
36 OXIDATIVE PHOSPHORYLATION 6 84 2.427e-05 0.003052
37 REGULATION OF PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL 10 280 2.369e-05 0.003052
38 NAD METABOLIC PROCESS 5 55 3.703e-05 0.004527
39 ANTIGEN PROCESSING AND PRESENTATION OF PEPTIDE ANTIGEN VIA MHC CLASS I 6 91 3.827e-05 0.004527
40 CELLULAR MACROMOLECULAR COMPLEX ASSEMBLY 16 727 3.892e-05 0.004527
41 POSITIVE REGULATION OF PROTEOLYSIS 11 363 4.17e-05 0.004733
42 REGULATION OF RNA STABILITY 7 139 4.883e-05 0.005163
43 NEGATIVE REGULATION OF PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL 7 139 4.883e-05 0.005163
44 NUCLEOSIDE PHOSPHATE BIOSYNTHETIC PROCESS 8 188 4.672e-05 0.005163
45 FC EPSILON RECEPTOR SIGNALING PATHWAY 7 142 5.593e-05 0.005699
46 REGULATION OF RESPONSE TO STRESS 24 1468 5.635e-05 0.005699
47 MITOCHONDRION ORGANIZATION 14 594 5.897e-05 0.005838
48 ANTIGEN RECEPTOR MEDIATED SIGNALING PATHWAY 8 195 6.047e-05 0.005862
49 POSITIVE REGULATION OF PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL 8 196 6.269e-05 0.005953
50 TRANSLATIONAL INITIATION 7 146 6.669e-05 0.006084
51 T CELL RECEPTOR SIGNALING PATHWAY 7 146 6.669e-05 0.006084
52 CELLULAR RESPONSE TO CYTOKINE STIMULUS 14 606 7.3e-05 0.006532
53 REGULATION OF PROTEIN UBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS 6 103 7.677e-05 0.00674
54 IMMUNE RESPONSE REGULATING CELL SURFACE RECEPTOR SIGNALING PATHWAY 10 323 7.881e-05 0.006791
55 ANTIGEN PROCESSING AND PRESENTATION OF EXOGENOUS PEPTIDE ANTIGEN VIA MHC CLASS I 5 66 8.957e-05 0.007443
56 REGULATION OF CELLULAR AMINO ACID METABOLIC PROCESS 5 66 8.957e-05 0.007443
57 POSITIVE REGULATION OF IMMUNE SYSTEM PROCESS 17 867 9.203e-05 0.00748
58 PHOSPHORYLATION 21 1228 9.324e-05 0.00748
59 CARBOHYDRATE DERIVATIVE METABOLIC PROCESS 19 1047 9.658e-05 0.007617
60 COFACTOR METABOLIC PROCESS 10 334 0.0001039 0.008055
61 PROTEASOME ASSEMBLY 3 14 0.0001083 0.008128
62 MITOCHONDRIAL ELECTRON TRANSPORT UBIQUINOL TO CYTOCHROME C 3 14 0.0001083 0.008128
63 CELLULAR RESPONSE TO ORGANIC SUBSTANCE 27 1848 0.0001236 0.009127
NumGOOverlapSizeP ValueAdj. P Value
1 RNA BINDING 44 1598 3.064e-16 2.846e-13
2 POLY A RNA BINDING 30 1170 2.578e-10 1.198e-07
3 TRANSLATION FACTOR ACTIVITY RNA BINDING 10 89 5.241e-10 1.623e-07
4 RIBONUCLEOTIDE BINDING 37 1860 1.761e-09 4.09e-07
5 ADENYL NUCLEOTIDE BINDING 32 1514 7.001e-09 1.301e-06
6 SNORNA BINDING 5 26 8.212e-07 0.0001272
7 TRANSLATION INITIATION FACTOR ACTIVITY 6 51 1.294e-06 0.0001717
8 HYDROLASE ACTIVITY ACTING ON ACID ANHYDRIDES 19 820 3.296e-06 0.0003827
9 TRANSLATION ELONGATION FACTOR ACTIVITY 4 20 9.375e-06 0.0009677
10 LIGASE ACTIVITY FORMING CARBON OXYGEN BONDS 5 44 1.228e-05 0.001141
11 SNRNA BINDING 4 34 8.331e-05 0.007036
NumGOOverlapSizeP ValueAdj. P Value
1 MITOCHONDRIAL PART 28 953 5.159e-11 3.013e-08
2 RIBONUCLEOPROTEIN COMPLEX 24 721 1.235e-10 3.607e-08
3 MITOCHONDRION 35 1633 7.792e-10 1.517e-07
4 PROTEASOME COMPLEX 9 76 2.461e-09 3.593e-07
5 MITOCHONDRIAL MATRIX 16 412 2.398e-08 2.334e-06
6 MYELIN SHEATH 11 168 2.247e-08 2.334e-06
7 ENVELOPE 23 1090 1.353e-06 0.0001129
8 ORGANELLE INNER MEMBRANE 15 525 3.254e-06 0.0002375
9 MITOCHONDRIAL ENVELOPE 17 691 5.176e-06 0.0003359
10 X90S PRERIBOSOME 4 24 2.013e-05 0.001069
11 PROTEASOME ACCESSORY COMPLEX 4 24 2.013e-05 0.001069
12 PROTEASOME REGULATORY PARTICLE BASE SUBCOMPLEX 3 12 6.612e-05 0.002978
13 NUCLEOLAR PART 5 62 6.63e-05 0.002978
14 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX 3 16 0.000165 0.006422
15 TRANSLATION PREINITIATION COMPLEX 3 16 0.000165 0.006422

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 Gap_junction_hsa04540 6 88 3.164e-05 0.001645
2 Phagosome_hsa04145 7 152 8.596e-05 0.002235
3 Tight_junction_hsa04530 6 170 0.001134 0.01965
4 Apoptosis_hsa04210 5 138 0.002624 0.03411
5 HIF_1_signaling_pathway_hsa04066 3 100 0.03142 0.3241
6 MAPK_signaling_pathway_hsa04010 5 295 0.05257 0.3241
7 Rap1_signaling_pathway_hsa04015 4 206 0.05342 0.3241
8 Autophagy_animal_hsa04140 3 128 0.05789 0.3241
9 VEGF_signaling_pathway_hsa04370 2 59 0.06187 0.3241
10 FoxO_signaling_pathway_hsa04068 3 132 0.06232 0.3241
11 Phospholipase_D_signaling_pathway_hsa04072 3 146 0.07901 0.37
12 mTOR_signaling_pathway_hsa04150 3 151 0.08539 0.37
13 PI3K_Akt_signaling_pathway_hsa04151 5 352 0.0948 0.3792
14 ErbB_signaling_pathway_hsa04012 2 85 0.1153 0.4284
15 NF_kappa_B_signaling_pathway_hsa04064 2 95 0.1382 0.479
16 Focal_adhesion_hsa04510 3 199 0.1564 0.5082
17 Regulation_of_actin_cytoskeleton_hsa04810 3 208 0.1713 0.524
18 Ras_signaling_pathway_hsa04014 3 232 0.2129 0.5825
19 Apelin_signaling_pathway_hsa04371 2 137 0.2414 0.6278
20 Jak_STAT_signaling_pathway_hsa04630 2 162 0.3048 0.7324
21 Necroptosis_hsa04217 2 164 0.3099 0.7324
22 Cytokine_cytokine_receptor_interaction_hsa04060 2 270 0.5543 1

Quest ID: 1087b676c38d13edd197d1011e19e4cf