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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-let-7a-5p IGF2BP3 0.62 3.0E-5 2.63 0.00021 MirTarget; TargetScan -0.74 0.0019 NA
2 hsa-miR-125a-5p IGF2BP3 0.6 0.01023 2.63 0.00021 miRanda -0.53 0.00038 NA
3 hsa-miR-320a IGF2BP3 0.44 0.03902 2.63 0.00021 miRNAWalker2 validate; MirTarget; PITA; miRanda; miRNATAP -0.61 0.0002 NA
4 hsa-miR-34a-5p IGF2BP3 1.9 0 2.63 0.00021 miRNAWalker2 validate -0.36 0.0089 NA
5 hsa-miR-429 IGF2BP3 4.49 0 2.63 0.00021 PITA; miRanda; miRNATAP -0.18 0.00509 NA
6 hsa-miR-592 IGF2BP3 1.52 0.00064 2.63 0.00021 PITA -0.16 0.04588 NA
7 hsa-miR-664a-3p IGF2BP3 0.63 0.0052 2.63 0.00021 MirTarget -0.68 1.0E-5 NA
8 hsa-miR-98-5p IGF2BP3 1.11 0 2.63 0.00021 MirTarget -0.36 0.04216 NA
NumGOOverlapSizeP ValueAdj. P Value
1 GLUCURONATE METABOLIC PROCESS 3 27 9.617e-06 0.004475
2 NEGATIVE REGULATION OF GENE EXPRESSION 11 1493 8.089e-06 0.004475
3 NEGATIVE REGULATION OF NITROGEN COMPOUND METABOLIC PROCESS 11 1517 9.422e-06 0.004475
4 POSITIVE REGULATION OF PROTEIN METABOLIC PROCESS 12 1492 1.054e-06 0.004475
5 RESPONSE TO GROWTH FACTOR 7 475 6.542e-06 0.004475
6 URONIC ACID METABOLIC PROCESS 3 27 9.617e-06 0.004475
7 REGULATION OF CELL DEATH 11 1472 7.061e-06 0.004475
8 NEGATIVE REGULATION OF PROTEIN METABOLIC PROCESS 10 1087 3.355e-06 0.004475
9 CELLULAR GLUCURONIDATION 3 22 5.09e-06 0.004475
10 RESPONSE TO MANGANESE ION 3 17 2.259e-06 0.004475
11 FLAVONOID METABOLIC PROCESS 3 28 1.076e-05 0.004551
12 CELLULAR RESPONSE TO ENDOGENOUS STIMULUS 9 1008 1.493e-05 0.005789
13 POSITIVE REGULATION OF TRANSMEMBRANE RECEPTOR PROTEIN SERINE THREONINE KINASE SIGNALING PATHWAY 4 100 1.669e-05 0.005973
14 ERBB2 SIGNALING PATHWAY 3 39 2.967e-05 0.0097
15 POSITIVE REGULATION OF CELL DEATH 7 605 3.127e-05 0.0097
NumGOOverlapSizeP ValueAdj. P Value
1 POLY A BINDING 3 13 9.542e-07 0.0008865
2 POLY PURINE TRACT BINDING 3 19 3.213e-06 0.001492
3 GLUCURONOSYLTRANSFERASE ACTIVITY 3 34 1.953e-05 0.004956
4 TRANSLATION REGULATOR ACTIVITY 3 35 2.134e-05 0.004956
NumGOOverlapSizeP ValueAdj. P Value
1 CYTOPLASMIC STRESS GRANULE 3 32 1.622e-05 0.009474

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 Adherens_junction_hsa04520 3 72 0.000187 0.007945
2 ErbB_signaling_pathway_hsa04012 3 85 0.0003056 0.007945
3 HIF_1_signaling_pathway_hsa04066 2 100 0.01047 0.1368
4 MAPK_signaling_pathway_hsa04010 3 295 0.01052 0.1368
5 PI3K_Akt_signaling_pathway_hsa04151 3 352 0.01688 0.1537
6 FoxO_signaling_pathway_hsa04068 2 132 0.01774 0.1537
7 Tight_junction_hsa04530 2 170 0.02842 0.2094
8 Calcium_signaling_pathway_hsa04020 2 182 0.03222 0.2094
9 Focal_adhesion_hsa04510 2 199 0.03792 0.2099
10 Rap1_signaling_pathway_hsa04015 2 206 0.04037 0.2099
11 Neuroactive_ligand_receptor_interaction_hsa04080 2 278 0.06877 0.3251

Quest ID: 33a86385653e13c73bc83c739fd2d140