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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 1.1 0.00082 -1.14 3.0E-5 miRNAWalker2 validate -0.19 0 NA
2 hsa-miR-320b NLRP3 0.23 0.37882 -1.14 3.0E-5 miRanda -0.16 0.00126 NA
3 hsa-miR-324-5p NLRP3 1.07 5.0E-5 -1.14 3.0E-5 miRanda -0.23 0 NA
4 hsa-miR-421 NLRP3 0.17 0.53528 -1.14 3.0E-5 miRanda -0.17 0.00078 NA
5 hsa-miR-429 NLRP3 2.38 0 -1.14 3.0E-5 miRanda -0.26 0 NA
NumGOOverlapSizeP ValueAdj. P Value
1 REGULATION OF PROTEIN STABILITY 10 221 3.336e-07 0.001552
2 COFACTOR METABOLIC PROCESS 11 334 1.95e-06 0.001814
3 SMALL MOLECULE METABOLIC PROCESS 26 1767 1.816e-06 0.001814
4 POSITIVE REGULATION OF BIOSYNTHETIC PROCESS 27 1805 7.891e-07 0.001814
5 NEGATIVE REGULATION OF APOPTOTIC SIGNALING PATHWAY 9 200 1.391e-06 0.001814
6 REGULATION OF RESPONSE TO STRESS 23 1468 2.893e-06 0.002244
7 NEGATIVE REGULATION OF CELL DEATH 17 872 4.203e-06 0.002794
8 NEGATIVE REGULATION OF PROTEIN METABOLIC PROCESS 19 1087 5.232e-06 0.003043
9 CELLULAR RESPONSE TO ORGANIC CYCLIC COMPOUND 12 465 8.021e-06 0.004133
10 RESPONSE TO ABIOTIC STIMULUS 18 1024 8.882e-06 0.004133
11 REGULATION OF CELL DEATH 22 1472 1.052e-05 0.004449
12 POSITIVE REGULATION OF GENE EXPRESSION 24 1733 1.389e-05 0.004972
13 AGING 9 264 1.33e-05 0.004972
14 MACROMOLECULAR COMPLEX ASSEMBLY 21 1398 1.607e-05 0.005343
15 PROTEIN COMPLEX SUBUNIT ORGANIZATION 22 1527 1.865e-05 0.005785
16 REGULATION OF CELLULAR RESPONSE TO STRESS 14 691 2.108e-05 0.006129
17 PROTEIN FOLDING IN ENDOPLASMIC RETICULUM 3 11 2.448e-05 0.006701
18 NUCLEOBASE CONTAINING SMALL MOLECULE METABOLIC PROCESS 12 535 3.215e-05 0.006872
19 PROTEIN COMPLEX BIOGENESIS 18 1132 3.397e-05 0.006872
20 ER NUCLEUS SIGNALING PATHWAY 4 34 3.291e-05 0.006872
21 CELL AGING 5 67 3.096e-05 0.006872
22 PROTEIN COMPLEX ASSEMBLY 18 1132 3.397e-05 0.006872
23 REGULATION OF APOPTOTIC SIGNALING PATHWAY 10 363 2.742e-05 0.006872
24 RESPONSE TO ENDOPLASMIC RETICULUM STRESS 8 233 3.893e-05 0.007548
25 NEGATIVE REGULATION OF GENE EXPRESSION 21 1493 4.255e-05 0.00792
26 ORGANIC ACID METABOLIC PROCESS 16 953 5.15e-05 0.009216
NumGOOverlapSizeP ValueAdj. P Value
1 STEROID HORMONE RECEPTOR BINDING 7 81 2.754e-07 0.0002559
2 RNA BINDING 25 1598 9.929e-07 0.0004612
3 POLY A RNA BINDING 20 1170 3.978e-06 0.0009238
4 RECEPTOR BINDING 23 1476 3.17e-06 0.0009238
5 HORMONE RECEPTOR BINDING 7 168 3.562e-05 0.006619
6 ANDROGEN RECEPTOR BINDING 4 39 5.718e-05 0.007588
7 MACROMOLECULAR COMPLEX BINDING 20 1399 5.331e-05 0.007588
NumGOOverlapSizeP ValueAdj. P Value
1 ENDOPLASMIC RETICULUM CHAPERONE COMPLEX 3 11 2.448e-05 0.009789
2 NUCLEOLUS 15 848 5.029e-05 0.009789
3 RIBONUCLEOPROTEIN COMPLEX 14 721 3.36e-05 0.009789

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 VEGF_signaling_pathway_hsa04370 4 59 0.0002912 0.01514
2 Mitophagy_animal_hsa04137 3 65 0.005246 0.09431
3 Regulation_of_actin_cytoskeleton_hsa04810 5 208 0.005441 0.09431
4 Apoptosis_multiple_species_hsa04215 2 33 0.01368 0.1778
5 Apoptosis_hsa04210 3 138 0.03885 0.3529
6 mTOR_signaling_pathway_hsa04150 3 151 0.04853 0.3529
7 Adherens_junction_hsa04520 2 72 0.05784 0.3529
8 Necroptosis_hsa04217 3 164 0.05927 0.3529
9 Tight_junction_hsa04530 3 170 0.06458 0.3529
10 Peroxisome_hsa04146 2 83 0.07416 0.3529
11 ErbB_signaling_pathway_hsa04012 2 85 0.07727 0.3529
12 Gap_junction_hsa04540 2 88 0.08201 0.3529
13 Focal_adhesion_hsa04510 3 199 0.09311 0.3529
14 Rap1_signaling_pathway_hsa04015 3 206 0.1007 0.3529
15 HIF_1_signaling_pathway_hsa04066 2 100 0.1018 0.3529
16 PI3K_Akt_signaling_pathway_hsa04151 4 352 0.1232 0.4005
17 Sphingolipid_signaling_pathway_hsa04071 2 118 0.1336 0.4086
18 Autophagy_animal_hsa04140 2 128 0.1521 0.4394
19 Signaling_pathways_regulating_pluripotency_of_stem_cells_hsa04550 2 139 0.173 0.4735
20 Wnt_signaling_pathway_hsa04310 2 146 0.1865 0.485
21 Ras_signaling_pathway_hsa04014 2 232 0.3571 0.8074
22 Endocytosis_hsa04144 2 244 0.3804 0.8242
23 MAPK_signaling_pathway_hsa04010 2 295 0.4747 0.8955

Quest ID: ac97ab82e54d2bc9acc6a36ccc30bf6a