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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-143-5p PER2 -0.43 0.00646 -0.67 0 mirMAP -0.11 0.00297 NA
2 hsa-miR-17-5p PER2 0.7 2.0E-5 -0.67 0 mirMAP -0.15 2.0E-5 NA
3 hsa-miR-181a-5p PER2 0.25 0.05519 -0.67 0 MirTarget; miRNATAP -0.18 9.0E-5 NA
4 hsa-miR-181b-5p PER2 0.49 0.00105 -0.67 0 MirTarget -0.19 0 NA
5 hsa-miR-181c-5p PER2 -0.01 0.96913 -0.67 0 MirTarget; miRNATAP -0.13 0.00027 NA
6 hsa-miR-181d-5p PER2 0.16 0.36381 -0.67 0 MirTarget -0.13 6.0E-5 NA
7 hsa-miR-21-5p PER2 1.51 0 -0.67 0 MirTarget -0.31 0 NA
8 hsa-miR-30d-3p PER2 -0.12 0.32955 -0.67 0 mirMAP -0.16 0.00063 NA
9 hsa-miR-30d-5p PER2 0.72 0 -0.67 0 MirTarget; miRNATAP -0.19 3.0E-5 NA
10 hsa-miR-3127-5p PER2 0.84 0 -0.67 0 mirMAP -0.12 0.00118 NA
11 hsa-miR-324-5p PER2 0.37 0.00592 -0.67 0 miRanda -0.29 0 NA
12 hsa-miR-339-5p PER2 0.28 0.03557 -0.67 0 miRanda -0.16 0.00032 NA
13 hsa-miR-660-5p PER2 0.99 0 -0.67 0 mirMAP -0.11 0.01016 NA
14 hsa-miR-92b-3p PER2 0.22 0.29619 -0.67 0 MirTarget; miRNATAP -0.13 1.0E-5 NA
15 hsa-miR-93-5p PER2 1.4 0 -0.67 0 mirMAP -0.16 8.0E-5 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 REGULATION OF RESPONSE TO STRESS 14 1468 1.01e-07 0.000386
2 MITOTIC CELL CYCLE CHECKPOINT 6 139 1.659e-07 0.000386
3 POSITIVE REGULATION OF CELL CYCLE ARREST 5 85 4.184e-07 0.0006489
4 RESPONSE TO EXTERNAL STIMULUS 14 1821 1.415e-06 0.0007317
5 MITOTIC CELL CYCLE 10 766 6.588e-07 0.0007317
6 REGULATION OF RELEASE OF CYTOCHROME C FROM MITOCHONDRIA 4 44 1.14e-06 0.0007317
7 NEGATIVE REGULATION OF MITOTIC CELL CYCLE 6 199 1.367e-06 0.0007317
8 REGULATION OF CELL CYCLE ARREST 5 108 1.38e-06 0.0007317
9 CELL CYCLE CHECKPOINT 6 194 1.179e-06 0.0007317
10 CELLULAR RESPONSE TO STRESS 13 1565 1.64e-06 0.000763
11 CELL CYCLE PROCESS 11 1081 1.881e-06 0.0007959
12 REGULATION OF CELLULAR RESPONSE TO STRESS 9 691 2.714e-06 0.001052
13 CELL DEATH 10 1001 7.283e-06 0.001883
14 AGING 6 264 6.982e-06 0.001883
15 REGULATION OF CELL DEATH 12 1472 5.727e-06 0.001883
16 SIGNAL TRANSDUCTION BY PROTEIN PHOSPHORYLATION 7 404 6.558e-06 0.001883
17 PHOSPHORYLATION 11 1228 6.453e-06 0.001883
18 REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 13 1784 7.046e-06 0.001883
19 G1 DNA DAMAGE CHECKPOINT 4 73 8.806e-06 0.00205
20 RESPONSE TO ABIOTIC STIMULUS 10 1024 8.896e-06 0.00205
21 SCF DEPENDENT PROTEASOMAL UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS 3 23 9.253e-06 0.00205
22 INTRACELLULAR SIGNAL TRANSDUCTION 12 1572 1.124e-05 0.002376
23 CELL CYCLE 11 1316 1.247e-05 0.002522
24 RESPONSE TO OXYGEN LEVELS 6 311 1.771e-05 0.003062
25 POSITIVE REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION 9 876 1.843e-05 0.003062
26 INTERSPECIES INTERACTION BETWEEN ORGANISMS 8 662 1.839e-05 0.003062
27 SYMBIOSIS ENCOMPASSING MUTUALISM THROUGH PARASITISM 8 662 1.839e-05 0.003062
28 REGULATION OF MITOTIC CELL CYCLE 7 468 1.703e-05 0.003062
29 MACROMOLECULAR COMPLEX ASSEMBLY 11 1398 2.201e-05 0.0032
30 POSITIVE REGULATION OF MULTICELLULAR ORGANISMAL PROCESS 11 1395 2.157e-05 0.0032
31 REGULATION OF CELL CYCLE PHASE TRANSITION 6 321 2.117e-05 0.0032
32 RESPONSE TO BIOTIC STIMULUS 9 886 2.017e-05 0.0032
33 SIGNAL TRANSDUCTION IN RESPONSE TO DNA DAMAGE 4 96 2.61e-05 0.00368
34 DEFENSE RESPONSE TO OTHER ORGANISM 7 505 2.776e-05 0.003763
35 NEGATIVE REGULATION OF CELL CYCLE G1 S PHASE TRANSITION 4 98 2.831e-05 0.003763
36 MITOTIC DNA INTEGRITY CHECKPOINT 4 100 3.065e-05 0.003961
37 PROTEIN PHOSPHORYLATION 9 944 3.327e-05 0.004183
38 NEGATIVE REGULATION OF CYTOKINE PRODUCTION 5 211 3.6e-05 0.004409
39 NEGATIVE REGULATION OF GENE EXPRESSION 11 1493 4.054e-05 0.004757
40 ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE 6 361 4.089e-05 0.004757
41 DEFENSE RESPONSE 10 1231 4.379e-05 0.00497
42 NEGATIVE REGULATION OF MULTICELLULAR ORGANISMAL PROCESS 9 983 4.567e-05 0.00506
43 REGULATION OF CYTOKINE PRODUCTION 7 563 5.539e-05 0.005994
44 CELLULAR RESPONSE TO ORGANIC SUBSTANCE 12 1848 5.677e-05 0.006003
45 POSITIVE REGULATION OF CELL CYCLE PROCESS 5 247 7.607e-05 0.007866
46 SIGNAL TRANSDUCTION BY P53 CLASS MEDIATOR 4 127 7.803e-05 0.007893
47 POSITIVE REGULATION OF CELL DIFFERENTIATION 8 823 8.621e-05 0.008535
48 NEGATIVE REGULATION OF PROTEIN METABOLIC PROCESS 9 1087 9.943e-05 0.009639
NumGOOverlapSizeP ValueAdj. P Value
NumGOOverlapSizeP ValueAdj. P Value

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 Apoptosis_hsa04210 4 138 0.0001077 0.005599
2 TGF_beta_signaling_pathway_hsa04350 3 84 0.0004617 0.012
3 HIF_1_signaling_pathway_hsa04066 3 100 0.0007682 0.01332
4 Cell_cycle_hsa04110 3 124 0.00143 0.01483
5 Apoptosis_multiple_species_hsa04215 2 33 0.001606 0.01483
6 FoxO_signaling_pathway_hsa04068 3 132 0.001711 0.01483
7 p53_signaling_pathway_hsa04115 2 68 0.00666 0.04948
8 Gap_junction_hsa04540 2 88 0.01094 0.07113
9 MAPK_signaling_pathway_hsa04010 3 295 0.01584 0.09151
10 Sphingolipid_signaling_pathway_hsa04071 2 118 0.01908 0.09898
11 Oocyte_meiosis_hsa04114 2 124 0.02094 0.09898
12 Wnt_signaling_pathway_hsa04310 2 146 0.02836 0.1229
13 Hippo_signaling_pathway_hsa04390 2 154 0.03128 0.1246
14 Cellular_senescence_hsa04218 2 160 0.03355 0.1246
15 Ras_signaling_pathway_hsa04014 2 232 0.06524 0.2262
16 Endocytosis_hsa04144 2 244 0.07123 0.2315
17 Cytokine_cytokine_receptor_interaction_hsa04060 2 270 0.08479 0.2449

lncRNA-mediated sponge

(Download full result)

Num lncRNA miRNAs           miRNAs count     Gene Sponge regulatory network lncRNA log2FC lncRNA pvalue Gene log2FC Gene pvalue lncRNA-gene Pearson correlation
1 RP11-12A2.3 hsa-miR-17-5p;hsa-miR-181a-5p;hsa-miR-181b-5p;hsa-miR-181c-5p;hsa-miR-181d-5p;hsa-miR-21-5p;hsa-miR-30d-5p;hsa-miR-339-5p;hsa-miR-660-5p;hsa-miR-92b-3p;hsa-miR-93-5p 11 PER2 Sponge network -4.779 0 -0.671 0 0.379

Quest ID: ca04de00f1fe32bce81b01280f84c81b