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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-342-3p DNMT3B 0.04 0.96022 -0.07 0.87297 miRanda -0.15 0.03459 NA
2 hsa-miR-375 DNMT3B -0.13 0.94672 -0.07 0.87297 miRNAWalker2 validate; miRanda -0.12 0.00614 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 REGULATION OF PEPTIDASE ACTIVITY 9 392 5.364e-09 2.496e-05
2 REGULATION OF CYSTEINE TYPE ENDOPEPTIDASE ACTIVITY 7 213 2.98e-08 6.933e-05
3 REGULATION OF PROTEOLYSIS 10 711 6.822e-08 0.0001058
4 POSITIVE REGULATION OF PEPTIDASE ACTIVITY 6 154 1.187e-07 0.0001105
5 REGULATION OF CELL DEATH 13 1472 1.036e-07 0.0001105
6 CELL DEATH 11 1001 1.571e-07 0.0001218
7 CELLULAR RESPONSE TO OXYGEN CONTAINING COMPOUND 10 799 2.024e-07 0.0001236
8 APOPTOTIC SIGNALING PATHWAY 7 289 2.39e-07 0.0001236
9 POSITIVE REGULATION OF CELL DEATH 9 605 2.221e-07 0.0001236
10 RESPONSE TO NITROGEN COMPOUND 10 859 3.951e-07 0.0001414
11 ACTIVATION OF CYSTEINE TYPE ENDOPEPTIDASE ACTIVITY 5 95 3.35e-07 0.0001414
12 NEGATIVE REGULATION OF EXTRINSIC APOPTOTIC SIGNALING PATHWAY 5 98 3.914e-07 0.0001414
13 RESPONSE TO KETONE 6 182 3.187e-07 0.0001414
14 NEGATIVE REGULATION OF CELL DEATH 10 872 4.536e-07 0.0001508
15 ZYMOGEN ACTIVATION 5 112 7.615e-07 0.0002362
16 ACTIVATION OF CYSTEINE TYPE ENDOPEPTIDASE ACTIVITY INVOLVED IN APOPTOTIC SIGNALING PATHWAY 3 13 9.542e-07 0.0002612
17 S ADENOSYLHOMOCYSTEINE METABOLIC PROCESS 3 13 9.542e-07 0.0002612
18 POSITIVE REGULATION OF PROTEIN METABOLIC PROCESS 12 1492 1.054e-06 0.000271
19 POSITIVE REGULATION OF PROTEOLYSIS 7 363 1.106e-06 0.000271
20 CELLULAR RESPONSE TO STRESS 12 1565 1.749e-06 0.000407
21 POSITIVE REGULATION OF CYSTEINE TYPE ENDOPEPTIDASE ACTIVITY INVOLVED IN APOPTOTIC SIGNALING PATHWAY 3 17 2.259e-06 0.0005006
22 NEGATIVE REGULATION OF PROTEIN METABOLIC PROCESS 10 1087 3.355e-06 0.0007097
23 REGULATION OF EXTRINSIC APOPTOTIC SIGNALING PATHWAY 5 153 3.551e-06 0.0007184
24 RESPONSE TO OXYGEN CONTAINING COMPOUND 11 1381 3.813e-06 0.0007393
25 REGULATION OF CYSTEINE TYPE ENDOPEPTIDASE ACTIVITY INVOLVED IN APOPTOTIC SIGNALING PATHWAY 3 22 5.09e-06 0.0009473
26 RESPONSE TO INCREASED OXYGEN LEVELS 3 23 5.847e-06 0.0009717
27 RESPONSE TO HORMONE 9 893 5.62e-06 0.0009717
28 RESPONSE TO HYPEROXIA 3 23 5.847e-06 0.0009717
29 RESPONSE TO ENDOGENOUS STIMULUS 11 1450 6.109e-06 0.0009801
30 RESPONSE TO INORGANIC SUBSTANCE 7 479 6.911e-06 0.001072
31 NEGATIVE REGULATION OF CELL COMMUNICATION 10 1192 7.627e-06 0.001145
32 RESPONSE TO STEROID HORMONE 7 497 8.792e-06 0.00124
33 CELLULAR RESPONSE TO OXIDATIVE STRESS 5 184 8.734e-06 0.00124
34 POSITIVE REGULATION OF REACTIVE OXYGEN SPECIES METABOLIC PROCESS 4 86 9.175e-06 0.001256
35 CELLULAR RESPONSE TO ORGANIC SUBSTANCE 12 1848 9.912e-06 0.001318
36 NEGATIVE REGULATION OF APOPTOTIC SIGNALING PATHWAY 5 200 1.308e-05 0.001691
37 CELLULAR RESPONSE TO ENDOGENOUS STIMULUS 9 1008 1.493e-05 0.001878
38 EXTRINSIC APOPTOTIC SIGNALING PATHWAY 4 99 1.604e-05 0.001964
39 CELLULAR RESPONSE TO HORMONE STIMULUS 7 552 1.736e-05 0.00197
40 RESPONSE TO ALCOHOL 6 362 1.694e-05 0.00197
41 REGULATION OF APOPTOTIC SIGNALING PATHWAY 6 363 1.721e-05 0.00197
42 NEURON PROJECTION REGENERATION 3 33 1.783e-05 0.001975
43 REGULATION OF HYDROLASE ACTIVITY 10 1327 1.956e-05 0.002068
44 NEGATIVE REGULATION OF EXTRINSIC APOPTOTIC SIGNALING PATHWAY VIA DEATH DOMAIN RECEPTORS 3 34 1.953e-05 0.002068
45 NEGATIVE REGULATION OF RESPONSE TO STIMULUS 10 1360 2.42e-05 0.002497
46 NEGATIVE REGULATION OF ORGANELLE ORGANIZATION 6 387 2.468e-05 0.002497
47 ONE CARBON METABOLIC PROCESS 3 37 2.528e-05 0.002503
48 GLAND DEVELOPMENT 6 395 2.769e-05 0.002684
49 RESPONSE TO PEPTIDE 6 404 3.142e-05 0.002925
50 RESPONSE TO TOXIC SUBSTANCE 5 241 3.206e-05 0.002925
51 MESODERM DEVELOPMENT 4 118 3.203e-05 0.002925
52 NEGATIVE REGULATION OF PROTEIN MODIFICATION PROCESS 7 616 3.508e-05 0.003139
53 RESPONSE TO LIPID 8 888 4.639e-05 0.004073
54 PROTEIN MATURATION 5 265 5.04e-05 0.004334
55 REGULATION OF ORGANELLE ORGANIZATION 9 1178 5.123e-05 0.004334
56 REGULATION OF CELL DIFFERENTIATION 10 1492 5.367e-05 0.004459
57 RESPONSE TO ORGANIC CYCLIC COMPOUND 8 917 5.825e-05 0.004738
58 CELLULAR RESPONSE TO PEPTIDE 5 274 5.906e-05 0.004738
59 CELLULAR RESPONSE TO LIPID 6 457 6.243e-05 0.004841
60 TISSUE DEVELOPMENT 10 1518 6.217e-05 0.004841
61 NEGATIVE REGULATION OF CELLULAR COMPONENT ORGANIZATION 7 684 6.813e-05 0.005197
62 REGULATION OF NITRIC OXIDE BIOSYNTHETIC PROCESS 3 53 7.495e-05 0.005535
63 NEGATIVE REGULATION OF AUTOPHAGY 3 53 7.495e-05 0.005535
64 REGULATION OF EXTRINSIC APOPTOTIC SIGNALING PATHWAY VIA DEATH DOMAIN RECEPTORS 3 55 8.376e-05 0.006089
65 REGULATION OF REACTIVE OXYGEN SPECIES METABOLIC PROCESS 4 152 8.6e-05 0.006156
66 REGENERATION 4 161 0.0001074 0.007518
67 CELLULAR RESPONSE TO NITROGEN COMPOUND 6 505 0.0001082 0.007518
68 CELLULAR RESPONSE TO HYDROGEN PEROXIDE 3 61 0.0001142 0.007813
69 POSITIVE REGULATION OF APOPTOTIC SIGNALING PATHWAY 4 171 0.0001356 0.009141
70 REGULATION OF REACTIVE OXYGEN SPECIES BIOSYNTHETIC PROCESS 3 65 0.000138 0.009173
71 TISSUE MORPHOGENESIS 6 533 0.0001454 0.009396
72 MESODERM MORPHOGENESIS 3 66 0.0001444 0.009396
73 RESPONSE TO METAL ION 5 333 0.0001478 0.009421
74 RESPONSE TO CORTICOSTEROID 4 176 0.0001515 0.009523
75 NEGATIVE REGULATION OF PHOSPHORUS METABOLIC PROCESS 6 541 0.0001577 0.009654
76 NEGATIVE REGULATION OF PHOSPHATE METABOLIC PROCESS 6 541 0.0001577 0.009654
NumGOOverlapSizeP ValueAdj. P Value
NumGOOverlapSizeP ValueAdj. P Value

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 Apoptosis_hsa04210 5 138 2.139e-06 0.0001112
2 p53_signaling_pathway_hsa04115 3 68 0.0001578 0.004104
3 Jak_STAT_signaling_pathway_hsa04630 3 162 0.001985 0.02138
4 PI3K_Akt_signaling_pathway_hsa04151 4 352 0.002039 0.02138
5 Necroptosis_hsa04217 3 164 0.002056 0.02138
6 TNF_signaling_pathway_hsa04668 2 108 0.01213 0.1051
7 FoxO_signaling_pathway_hsa04068 2 132 0.01774 0.1271
8 Signaling_pathways_regulating_pluripotency_of_stem_cells_hsa04550 2 139 0.01955 0.1271
9 Cytokine_cytokine_receptor_interaction_hsa04060 2 270 0.06535 0.3113

Quest ID: 8737dea780a4b5c8baadfb7730ed967e