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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-320b NLRP3 -0.46 0.60626 -1.64 0.18701 miRanda -0.2 0.04187 NA
2 hsa-miR-3613-3p NLRP3 -0.82 0.21139 -1.64 0.18701 mirMAP -0.19 0.0409 NA
3 hsa-miR-429 NLRP3 2.04 0.58444 -1.64 0.18701 miRanda -0.4 0 NA
4 hsa-miR-935 NLRP3 0.35 0.75782 -1.64 0.18701 miRNATAP -0.11 0.02718 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 CELL DEATH 15 1001 6.446e-09 2.999e-05
2 MACROMOLECULAR COMPLEX ASSEMBLY 16 1398 7.903e-08 0.0001226
3 NEGATIVE REGULATION OF RESPONSE TO STIMULUS 16 1360 5.391e-08 0.0001226
4 PROTEIN COMPLEX BIOGENESIS 14 1132 2.517e-07 0.0002342
5 PROTEIN COMPLEX ASSEMBLY 14 1132 2.517e-07 0.0002342
6 SMALL MOLECULE METABOLIC PROCESS 17 1767 3.351e-07 0.0002599
7 NEGATIVE REGULATION OF APOPTOTIC SIGNALING PATHWAY 7 200 4.684e-07 0.0003114
8 REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION 16 1656 7.95e-07 0.000411
9 PROTEIN OLIGOMERIZATION 9 434 7.78e-07 0.000411
10 SMALL MOLECULE BIOSYNTHETIC PROCESS 9 443 9.226e-07 0.0004293
11 NEGATIVE REGULATION OF GENE EXPRESSION 15 1493 1.204e-06 0.0004474
12 COFACTOR METABOLIC PROCESS 8 334 1.173e-06 0.0004474
13 REGULATION OF INTRINSIC APOPTOTIC SIGNALING PATHWAY 6 145 1.25e-06 0.0004474
14 PROTEIN COMPLEX SUBUNIT ORGANIZATION 15 1527 1.598e-06 0.0005313
15 ORGANIC ACID METABOLIC PROCESS 12 953 1.817e-06 0.0005637
16 TISSUE REMODELING 5 87 2.049e-06 0.0005959
17 REGULATION OF APOPTOTIC SIGNALING PATHWAY 8 363 2.183e-06 0.0005976
18 NEGATIVE REGULATION OF INTRINSIC APOPTOTIC SIGNALING PATHWAY 5 90 2.424e-06 0.0006267
19 NEGATIVE REGULATION OF CELL COMMUNICATION 13 1192 3.052e-06 0.0007475
20 POSITIVE REGULATION OF DNA METABOLIC PROCESS 6 185 5.133e-06 0.001194
21 REGULATION OF RESPONSE TO STRESS 14 1468 5.562e-06 0.001214
22 REGULATION OF CELL DEATH 14 1472 5.74e-06 0.001214
23 NEGATIVE REGULATION OF PROTEIN METABOLIC PROCESS 12 1087 7.054e-06 0.001427
24 NEGATIVE REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION 8 437 8.547e-06 0.001657
25 HOMEOSTATIC PROCESS 13 1337 1.068e-05 0.001911
26 REGULATION OF B CELL APOPTOTIC PROCESS 3 18 1.032e-05 0.001911
27 REGULATION OF CYSTEINE TYPE ENDOPEPTIDASE ACTIVITY 6 213 1.149e-05 0.00198
28 REGULATION OF CYTOPLASMIC TRANSPORT 8 481 1.711e-05 0.002844
29 REGULATION OF MITOCHONDRIAL MEMBRANE PERMEABILITY INVOLVED IN APOPTOTIC PROCESS 3 22 1.935e-05 0.003105
30 MONOCARBOXYLIC ACID METABOLIC PROCESS 8 503 2.359e-05 0.003658
31 DEFENSE RESPONSE 12 1231 2.463e-05 0.003666
32 NEGATIVE REGULATION OF NUCLEOCYTOPLASMIC TRANSPORT 4 71 2.521e-05 0.003666
33 PROTEIN HOMOOLIGOMERIZATION 6 248 2.715e-05 0.003828
34 POSITIVE REGULATION OF IMMUNE SYSTEM PROCESS 10 867 3.249e-05 0.004446
35 NEGATIVE REGULATION OF CELL DEATH 10 872 3.412e-05 0.004536
36 REGULATION OF CELLULAR LOCALIZATION 12 1277 3.539e-05 0.004574
37 COENZYME METABOLIC PROCESS 6 265 3.935e-05 0.004948
38 REGULATION OF DNA REPLICATION 5 161 4.113e-05 0.005036
39 CARBOXYLIC ACID BIOSYNTHETIC PROCESS 6 270 4.367e-05 0.00508
40 ORGANIC ACID BIOSYNTHETIC PROCESS 6 270 4.367e-05 0.00508
41 POSITIVE REGULATION OF DNA REPLICATION 4 86 5.367e-05 0.005864
42 REGULATION OF RESPONSE TO EXTERNAL STIMULUS 10 926 5.67e-05 0.005864
43 MONOCARBOXYLIC ACID BIOSYNTHETIC PROCESS 5 172 5.634e-05 0.005864
44 REGULATION OF BINDING 6 283 5.671e-05 0.005864
45 POSITIVE REGULATION OF IMMUNE RESPONSE 8 563 5.247e-05 0.005864
46 MITOCHONDRIAL MEMBRANE ORGANIZATION 4 92 6.988e-05 0.007068
47 FATTY ACID METABOLIC PROCESS 6 296 7.27e-05 0.007197
48 REGULATION OF PROTEIN IMPORT 5 183 7.558e-05 0.007327
49 NEGATIVE REGULATION OF INTRACELLULAR PROTEIN TRANSPORT 4 95 7.92e-05 0.00737
50 REGULATION OF TRANSCRIPTION FACTOR IMPORT INTO NUCLEUS 4 95 7.92e-05 0.00737
51 REGULATION OF KINASE ACTIVITY 9 776 8.191e-05 0.007382
52 POSITIVE REGULATION OF CYTOKINE SECRETION 4 96 8.249e-05 0.007382
53 INFLAMMATORY RESPONSE 7 454 9.767e-05 0.008575
54 REGULATION OF INTRACELLULAR TRANSPORT 8 621 0.000104 0.008966
55 NEGATIVE REGULATION OF TRANSCRIPTION FACTOR IMPORT INTO NUCLEUS 3 39 0.0001116 0.00943
56 RESPONSE TO MOLECULE OF BACTERIAL ORIGIN 6 321 0.0001135 0.00943
57 POSITIVE REGULATION OF RESPONSE TO STIMULUS 14 1929 0.0001181 0.009644
58 CYTOPLASMIC SEQUESTERING OF PROTEIN 3 40 0.0001204 0.009661
NumGOOverlapSizeP ValueAdj. P Value
NumGOOverlapSizeP ValueAdj. P Value

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 VEGF_signaling_pathway_hsa04370 4 59 1.206e-05 0.0006272
2 Regulation_of_actin_cytoskeleton_hsa04810 5 208 0.000138 0.003178
3 Sphingolipid_signaling_pathway_hsa04071 4 118 0.0001833 0.003178
4 Mitophagy_animal_hsa04137 3 65 0.0005105 0.006348
5 Adherens_junction_hsa04520 3 72 0.0006888 0.006348
6 Tight_junction_hsa04530 4 170 0.0007325 0.006348
7 ErbB_signaling_pathway_hsa04012 3 85 0.001116 0.007593
8 Gap_junction_hsa04540 3 88 0.001234 0.007593
9 Focal_adhesion_hsa04510 4 199 0.001314 0.007593
10 Rap1_signaling_pathway_hsa04015 4 206 0.001492 0.007759
11 Apoptosis_hsa04210 3 138 0.004431 0.01959
12 Signaling_pathways_regulating_pluripotency_of_stem_cells_hsa04550 3 139 0.004521 0.01959
13 mTOR_signaling_pathway_hsa04150 3 151 0.005691 0.02276
14 Necroptosis_hsa04217 3 164 0.007146 0.02654
15 Peroxisome_hsa04146 2 83 0.01696 0.05881
16 Ras_signaling_pathway_hsa04014 3 232 0.01817 0.05904
17 HIF_1_signaling_pathway_hsa04066 2 100 0.02405 0.07356
18 MAPK_signaling_pathway_hsa04010 3 295 0.03374 0.09748
19 Autophagy_animal_hsa04140 2 128 0.03786 0.1036
20 FoxO_signaling_pathway_hsa04068 2 132 0.04003 0.1041
21 Apelin_signaling_pathway_hsa04371 2 137 0.04281 0.106
22 Phospholipase_D_signaling_pathway_hsa04072 2 146 0.04799 0.1085
23 Wnt_signaling_pathway_hsa04310 2 146 0.04799 0.1085
24 Phagosome_hsa04145 2 152 0.05156 0.1088
25 PI3K_Akt_signaling_pathway_hsa04151 3 352 0.05229 0.1088
26 Cellular_senescence_hsa04218 2 160 0.05647 0.1129
27 cAMP_signaling_pathway_hsa04024 2 198 0.08181 0.1519
28 Endocytosis_hsa04144 2 244 0.1162 0.2014

Quest ID: 1c24d48942c9574aaa45a787b9990374