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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-193b-3p NLRP3 1.98 0 -2.48 0 miRNAWalker2 validate -0.35 0 NA
2 hsa-miR-28-5p NLRP3 0.19 0.02781 -2.48 0 miRanda -0.76 0 NA
3 hsa-miR-320a NLRP3 0.25 0.06954 -2.48 0 miRanda -0.3 0.00266 NA
4 hsa-miR-320b NLRP3 1.16 0 -2.48 0 miRanda -0.34 0 NA
5 hsa-miR-324-5p NLRP3 1.22 0 -2.48 0 miRanda -0.7 0 NA
6 hsa-miR-421 NLRP3 1.17 0 -2.48 0 miRanda -0.58 0 NA
7 hsa-miR-429 NLRP3 1.44 0 -2.48 0 miRanda -0.58 0 NA
8 hsa-miR-589-3p NLRP3 1.64 0 -2.48 0 MirTarget -0.51 0 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 AGING 13 264 5.582e-09 8.657e-06
2 REGULATION OF CELLULAR RESPONSE TO STRESS 20 691 3.816e-09 8.657e-06
3 REGULATION OF APOPTOTIC SIGNALING PATHWAY 15 363 3.811e-09 8.657e-06
4 REGULATION OF CELL DEATH 28 1472 2.301e-08 2.417e-05
5 REGULATION OF CELLULAR PROTEIN LOCALIZATION 17 552 2.597e-08 2.417e-05
6 NEGATIVE REGULATION OF CELL DEATH 21 872 3.659e-08 2.432e-05
7 REGULATION OF PROTEIN LOCALIZATION 22 950 3.306e-08 2.432e-05
8 REGULATION OF CYSTEINE TYPE ENDOPEPTIDASE ACTIVITY 11 213 5.456e-08 3.173e-05
9 CELL DEATH 22 1001 8.292e-08 4.287e-05
10 NEGATIVE REGULATION OF APOPTOTIC SIGNALING PATHWAY 10 200 3.049e-07 0.0001419
11 COFACTOR METABOLIC PROCESS 12 334 6.767e-07 0.0002422
12 REGULATION OF MITOCHONDRION ORGANIZATION 10 218 6.733e-07 0.0002422
13 REGULATION OF PROTEIN LOCALIZATION TO NUCLEUS 10 218 6.733e-07 0.0002422
14 EXECUTION PHASE OF APOPTOSIS 6 55 8.498e-07 0.0002824
15 REGULATION OF CELLULAR LOCALIZATION 23 1277 1.356e-06 0.0004207
16 POSITIVE REGULATION OF CELLULAR PROTEIN LOCALIZATION 12 360 1.485e-06 0.0004214
17 POSITIVE REGULATION OF BIOSYNTHETIC PROCESS 28 1805 1.54e-06 0.0004214
18 NEGATIVE REGULATION OF RESPONSE TO OXIDATIVE STRESS 5 35 1.85e-06 0.000453
19 NEGATIVE REGULATION OF CELLULAR RESPONSE TO OXIDATIVE STRESS 5 35 1.85e-06 0.000453
20 REGULATION OF INTRINSIC APOPTOTIC SIGNALING PATHWAY 8 145 2.349e-06 0.0005465
21 REGULATION OF PEPTIDASE ACTIVITY 12 392 3.578e-06 0.0007928
22 REGULATION OF RESPONSE TO STRESS 24 1468 4.166e-06 0.0008811
23 PROTEIN LOCALIZATION TO ORGANELLE 14 556 5.146e-06 0.001041
24 NEGATIVE REGULATION OF OXIDATIVE STRESS INDUCED INTRINSIC APOPTOTIC SIGNALING PATHWAY 4 21 6.377e-06 0.001236
25 POSITIVE REGULATION OF MITOCHONDRION ORGANIZATION 8 167 6.705e-06 0.001248
26 REGULATION OF OXIDATIVE STRESS INDUCED CELL DEATH 5 46 7.418e-06 0.001327
27 RESPONSE TO ABIOTIC STIMULUS 19 1024 8.47e-06 0.00146
28 HOMEOSTATIC PROCESS 22 1337 1.019e-05 0.001692
29 MITOCHONDRION ORGANIZATION 14 594 1.088e-05 0.001692
30 POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION 13 514 1.091e-05 0.001692
31 REGULATION OF PROTEIN TARGETING 10 307 1.417e-05 0.002127
32 NEGATIVE REGULATION OF INTRINSIC APOPTOTIC SIGNALING PATHWAY 6 90 1.543e-05 0.002244
33 MITOCHONDRIAL MEMBRANE ORGANIZATION 6 92 1.751e-05 0.002376
34 REGULATION OF ORGANELLE ORGANIZATION 20 1178 1.749e-05 0.002376
35 REGULATION OF INTRACELLULAR TRANSPORT 14 621 1.787e-05 0.002376
36 REGULATION OF NEURON DEATH 9 252 1.88e-05 0.00243
37 NEGATIVE REGULATION OF PROTEIN METABOLIC PROCESS 19 1087 1.956e-05 0.002459
38 REGULATION OF OXIDATIVE STRESS INDUCED INTRINSIC APOPTOTIC SIGNALING PATHWAY 4 29 2.44e-05 0.002988
39 REGULATION OF CYTOPLASMIC TRANSPORT 12 481 2.774e-05 0.00331
40 POSITIVE REGULATION OF ORGANELLE ORGANIZATION 13 573 3.403e-05 0.003959
41 PROTEIN IMPORT 7 155 3.765e-05 0.004272
42 REGULATION OF CELL CYCLE 17 949 4.148e-05 0.004488
43 REGULATION OF RESPONSE TO OXIDATIVE STRESS 5 65 4.088e-05 0.004488
44 PROTEIN LOCALIZATION 25 1805 4.373e-05 0.004625
45 POSITIVE REGULATION OF RESPONSE TO STIMULUS 26 1929 4.722e-05 0.00479
46 CELL AGING 5 67 4.735e-05 0.00479
47 REGULATION OF NUCLEOCYTOPLASMIC TRANSPORT 8 220 4.894e-05 0.004845
48 REGULATION OF PROTEIN STABILITY 8 221 5.053e-05 0.004898
49 ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE 10 361 5.615e-05 0.005123
50 NEGATIVE REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION 11 437 5.616e-05 0.005123
51 APOPTOTIC SIGNALING PATHWAY 9 289 5.481e-05 0.005123
52 SMALL MOLECULE BIOSYNTHETIC PROCESS 11 443 6.345e-05 0.005678
53 NEGATIVE REGULATION OF NEURON DEATH 7 171 7.021e-05 0.006164
54 REGULATION OF PROTEOLYSIS 14 711 7.772e-05 0.006697
55 HOMEOSTASIS OF NUMBER OF CELLS 7 175 8.12e-05 0.006869
56 POSITIVE REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 17 1004 8.315e-05 0.006909
57 SMALL MOLECULE METABOLIC PROCESS 24 1767 8.725e-05 0.006927
58 POLYAMINE METABOLIC PROCESS 3 15 8.65e-05 0.006927
59 REGULATION OF INTRACELLULAR PROTEIN TRANSPORT 10 381 8.784e-05 0.006927
60 REGULATION OF MITOTIC CELL CYCLE 11 468 0.0001033 0.008011
61 REGULATION OF RESPONSE TO EXTERNAL STIMULUS 16 926 0.0001086 0.008018
62 REGULATION OF MITOPHAGY 4 42 0.0001084 0.008018
63 REGULATION OF PROTEIN IMPORT 7 183 0.0001074 0.008018
64 REGULATION OF AUTOPHAGY 8 249 0.0001162 0.008445
65 NEGATIVE REGULATION OF CELL AGING 3 17 0.0001282 0.009036
66 PROTEIN STABILIZATION 6 131 0.0001273 0.009036
NumGOOverlapSizeP ValueAdj. P Value
1 POLY A RNA BINDING 21 1170 4.448e-06 0.002552
2 RNA BINDING 25 1598 5.494e-06 0.002552
NumGOOverlapSizeP ValueAdj. P Value
1 MITOCHONDRION 26 1633 2.473e-06 0.001444

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 VEGF_signaling_pathway_hsa04370 5 59 2.549e-05 0.0007323
2 HIF_1_signaling_pathway_hsa04066 6 100 2.817e-05 0.0007323
3 Autophagy_animal_hsa04140 6 128 0.0001121 0.001943
4 Mitophagy_animal_hsa04137 4 65 0.0005906 0.007678
5 Apoptosis_hsa04210 5 138 0.001364 0.01418
6 Necroptosis_hsa04217 5 164 0.002898 0.02512
7 MAPK_signaling_pathway_hsa04010 6 295 0.008139 0.05759
8 Apelin_signaling_pathway_hsa04371 4 137 0.00886 0.05759
9 ErbB_signaling_pathway_hsa04012 3 85 0.01393 0.07647
10 Autophagy_other_hsa04136 2 32 0.01525 0.07647
11 Apoptosis_multiple_species_hsa04215 2 33 0.01618 0.07647
12 PI3K_Akt_signaling_pathway_hsa04151 6 352 0.01812 0.07854
13 Ferroptosis_hsa04216 2 40 0.02327 0.09306
14 Focal_adhesion_hsa04510 4 199 0.03036 0.11
15 Sphingolipid_signaling_pathway_hsa04071 3 118 0.03275 0.11
16 Rap1_signaling_pathway_hsa04015 4 206 0.03384 0.11
17 Ras_signaling_pathway_hsa04014 4 232 0.04871 0.149
18 mTOR_signaling_pathway_hsa04150 3 151 0.06015 0.1738
19 Jak_STAT_signaling_pathway_hsa04630 3 162 0.07106 0.1945
20 TNF_signaling_pathway_hsa04668 2 108 0.1336 0.3473
21 AMPK_signaling_pathway_hsa04152 2 121 0.16 0.3963
22 FoxO_signaling_pathway_hsa04068 2 132 0.1831 0.4328
23 Signaling_pathways_regulating_pluripotency_of_stem_cells_hsa04550 2 139 0.198 0.4477
24 Phospholipase_D_signaling_pathway_hsa04072 2 146 0.2131 0.4617
25 Cellular_senescence_hsa04218 2 160 0.2435 0.5065
26 cAMP_signaling_pathway_hsa04024 2 198 0.3263 0.6237
27 Regulation_of_actin_cytoskeleton_hsa04810 2 208 0.3478 0.6237
28 Endocytosis_hsa04144 2 244 0.4231 0.6667

Quest ID: 9a287492f8e672a088ec1e46f770e2a0