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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-27a-3p BMI1 0.09 0.95011 -0.05 0.94796 miRNAWalker2 validate -0.12 0.00918 NA
2 hsa-let-7b-5p CBX2 0.16 0.92777 -0.43 0.46513 miRNATAP -0.3 0.00188 NA
3 hsa-miR-192-3p CBX2 0.29 0.43172 -0.43 0.46513 mirMAP -0.13 0.00014 NA
4 hsa-miR-29a-3p CBX2 0.14 0.92846 -0.43 0.46513 miRNATAP -0.24 0.00099 NA
5 hsa-miR-30a-5p CBX2 0.28 0.86479 -0.43 0.46513 miRNATAP -0.23 1.0E-5 NA
6 hsa-miR-582-3p CBX2 0 0.99857 -0.43 0.46513 mirMAP -0.1 0.01531 NA
7 hsa-miR-328-3p CBX4 0.08 0.88063 -0.24 0.72041 miRNAWalker2 validate -0.11 0.00584 NA
8 hsa-miR-497-5p CBX4 0.03 0.96083 -0.24 0.72041 MirTarget; miRNATAP -0.11 0.0007 NA
9 hsa-let-7e-5p EZH2 0.2 0.87709 -0.16 0.82451 miRNATAP -0.21 0.00023 NA
10 hsa-miR-139-5p EZH2 -0.15 0.79074 -0.16 0.82451 miRanda -0.15 0.00087 NA
11 hsa-miR-149-5p PHC1 -0.27 0.7308 0.12 0.81657 miRNATAP -0.1 0.00095 NA
12 hsa-miR-20a-5p PHC1 0.01 0.99178 0.12 0.81657 miRNAWalker2 validate -0.1 0.0433 NA
13 hsa-miR-22-3p PHC1 -0.08 0.96949 0.12 0.81657 MirTarget -0.49 0 NA
14 hsa-miR-24-3p PHC1 -0 0.99748 0.12 0.81657 miRNATAP -0.41 0 NA
15 hsa-miR-29a-3p PHC1 0.14 0.92846 0.12 0.81657 MirTarget -0.21 4.0E-5 NA
16 hsa-miR-29b-3p PHC1 0.14 0.9001 0.12 0.81657 MirTarget -0.21 6.0E-5 NA
17 hsa-miR-339-5p PHC1 -0.04 0.94751 0.12 0.81657 MirTarget; miRanda -0.17 0.00094 NA
18 hsa-miR-421 PHC1 -0.1 0.66357 0.12 0.81657 miRanda -0.17 0.00052 NA
19 hsa-miR-590-3p PHC1 -0.14 0.70045 0.12 0.81657 mirMAP -0.23 5.0E-5 NA
20 hsa-miR-940 PHC1 -0.21 0.49157 0.12 0.81657 MirTarget; PITA; miRNATAP -0.12 0.00123 NA
21 hsa-miR-181a-5p RNF2 0.13 0.91726 -0.16 0.79096 miRTarBase -0.11 0.00314 NA
22 hsa-miR-186-5p RNF2 -0.03 0.97568 -0.16 0.79096 miRNAWalker2 validate; MirTarget -0.14 0.00759 NA
23 hsa-miR-26b-5p RNF2 -0.01 0.99661 -0.16 0.79096 miRNAWalker2 validate -0.11 0.00674 NA
24 hsa-miR-374a-5p RNF2 -0.06 0.93171 -0.16 0.79096 mirMAP -0.12 0.0119 NA
25 hsa-miR-29a-5p SUZ12 0.18 0.58353 0.05 0.95147 MirTarget -0.11 0.00025 NA
NumGOOverlapSizeP ValueAdj. P Value
1 CHROMATIN MODIFICATION 7 539 9.94e-12 4.625e-08
2 CHROMATIN ORGANIZATION 7 663 4.266e-11 9.925e-08
3 PEPTIDYL LYSINE MODIFICATION 6 312 9.494e-11 1.394e-07
4 PROTEIN SUMOYLATION 5 115 1.198e-10 1.394e-07
5 CHROMOSOME ORGANIZATION 7 1009 8.155e-10 7.589e-07
6 NEGATIVE REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 6 740 1.706e-08 1.323e-05
7 PEPTIDYL AMINO ACID MODIFICATION 6 841 3.668e-08 2.438e-05
8 PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL 6 873 4.586e-08 2.667e-05
9 HISTONE UBIQUITINATION 3 34 1.564e-07 8.085e-05
10 NEGATIVE REGULATION OF GENE EXPRESSION 6 1493 1.124e-06 0.0005225
11 NEGATIVE REGULATION OF NITROGEN COMPOUND METABOLIC PROCESS 6 1517 1.235e-06 0.0005225
12 COVALENT CHROMATIN MODIFICATION 4 345 2.923e-06 0.001134
13 REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 6 1784 3.232e-06 0.001157
14 NEGATIVE REGULATION OF GENE EXPRESSION EPIGENETIC 3 112 5.887e-06 0.001956
NumGOOverlapSizeP ValueAdj. P Value
1 CHROMATIN BINDING 6 435 7.032e-10 6.533e-07
2 METHYLATED HISTONE BINDING 3 52 5.76e-07 0.0002364
3 MACROMOLECULAR COMPLEX BINDING 6 1399 7.634e-07 0.0002364
4 HISTONE BINDING 3 177 2.324e-05 0.005397
NumGOOverlapSizeP ValueAdj. P Value
1 PCG PROTEIN COMPLEX 7 43 1.27e-19 7.418e-17
2 PRC1 COMPLEX 5 12 6.236e-16 1.821e-13
3 NUCLEAR UBIQUITIN LIGASE COMPLEX 5 42 6.682e-13 1.301e-10
4 TRANSFERASE COMPLEX 7 703 6.441e-11 9.403e-09
5 CATALYTIC COMPLEX 7 1038 9.95e-10 1.162e-07
6 UBIQUITIN LIGASE COMPLEX 5 262 7.634e-09 7.431e-07
7 HETEROCHROMATIN 3 67 1.246e-06 0.0001039
8 HISTONE METHYLTRANSFERASE COMPLEX 3 71 1.485e-06 0.0001084
9 METHYLTRANSFERASE COMPLEX 3 90 3.044e-06 0.0001975
10 CHROMATIN 4 441 7.744e-06 0.0004522
11 ESC E Z COMPLEX 2 16 1.257e-05 0.0006674
12 SEX CHROMOSOME 2 27 3.67e-05 0.001786
13 NUCLEAR HETEROCHROMATIN 2 32 5.182e-05 0.002018
14 NUCLEOPLASM PART 4 708 5.004e-05 0.002018
15 EUCHROMATIN 2 31 4.859e-05 0.002018
16 NUCLEAR CHROMATIN 3 291 0.0001022 0.00373
17 CHROMOSOME 4 880 0.0001171 0.004023

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value

Quest ID: d2c5175d40c18eed5fcd6398989528a4