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show label of nodes with degree >=

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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-106b-5p APC 0.01 0.99606 -0.13 0.84689 miRNAWalker2 validate; miRTarBase -0.22 0 23087084 miR 106b downregulates adenomatous polyposis coli and promotes cell proliferation in human hepatocellular carcinoma; Moreover we demonstrated that miR-106b downregulates APC expression by directly targeting the 3'-untranslated region of APC messenger RNA; Taken together our results suggest that miR-106b plays an important role in promoting the proliferation of human hepatoma cells and presents a novel mechanism of micro RNA-mediated direct suppression of APC expression in cancer cells
2 hsa-miR-148a-3p APC 0.1 0.96257 -0.13 0.84689 miRNAWalker2 validate -0.12 0.00641 NA
3 hsa-miR-154-3p APC 0.16 0.45688 -0.13 0.84689 TargetScan -0.12 0.00356 NA
4 hsa-miR-192-5p APC 0.07 0.97377 -0.13 0.84689 miRNAWalker2 validate -0.11 0.00054 NA
5 hsa-miR-193a-3p APC -0.08 0.83305 -0.13 0.84689 miRanda -0.15 0.00011 NA
6 hsa-miR-27a-3p APC 0.03 0.98139 -0.13 0.84689 miRNAWalker2 validate; miRTarBase; miRNATAP -0.17 0.00984 22018270 Finally the APC gene was identified as the direct and functional target of miR-27
7 hsa-miR-335-3p APC -0.17 0.87115 -0.13 0.84689 mirMAP -0.21 0 NA
8 hsa-miR-374a-5p APC -0.23 0.75404 -0.13 0.84689 mirMAP -0.28 0 NA
9 hsa-miR-374b-5p APC -0.27 0.75538 -0.13 0.84689 mirMAP -0.2 0.00044 NA
10 hsa-miR-421 APC -0.23 0.52658 -0.13 0.84689 miRanda -0.15 0.0002 NA
11 hsa-miR-450b-5p APC 0.15 0.72052 -0.13 0.84689 miRNATAP -0.17 6.0E-5 NA
12 hsa-miR-501-3p APC -0.13 0.86326 -0.13 0.84689 TargetScan -0.12 0.00171 NA
13 hsa-miR-590-3p APC 0.08 0.81071 -0.13 0.84689 PITA; miRanda; mirMAP; miRNATAP -0.1 0.00339 NA
NumGOOverlapSizeP ValueAdj. P Value
NumGOOverlapSizeP ValueAdj. P Value
NumGOOverlapSizeP ValueAdj. P Value
1 CYTOPLASMIC MICROTUBULE 3 57 1.821e-06 0.001064
2 BETA CATENIN DESTRUCTION COMPLEX 2 14 1.634e-05 0.00477

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 Signaling_pathways_regulating_pluripotency_of_stem_cells_hsa04550 2 139 0.001672 0.03548
2 Wnt_signaling_pathway_hsa04310 2 146 0.001842 0.03548
3 Hippo_signaling_pathway_hsa04390 2 154 0.002047 0.03548

lncRNA-mediated sponge

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Num lncRNA miRNAs           miRNAs count     Gene Sponge regulatory network lncRNA log2FC lncRNA pvalue Gene log2FC Gene pvalue lncRNA-gene Pearson correlation

Quest ID: bdeda62098e919f40aa0a1e76fd9841a