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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-7e-5p RRM2 -0.73 0 2.68 0 miRNATAP -0.68 0 NA
2 hsa-let-7g-5p RRM2 -0.74 0 2.68 0 miRNAWalker2 validate; miRNATAP -0.44 0.00032 NA
3 hsa-miR-125a-5p RRM2 -0.56 0 2.68 0 miRanda -1.14 0 NA
4 hsa-miR-199a-5p RRM2 -1.65 0 2.68 0 miRanda -0.32 0 NA
5 hsa-miR-20b-5p RRM2 -1.3 0 2.68 0 miRNATAP -0.29 9.0E-5 NA
6 hsa-miR-26a-5p RRM2 -0.2 0.00167 2.68 0 miRNAWalker2 validate -0.78 4.0E-5 NA
7 hsa-miR-30a-5p RRM2 -0.78 0 2.68 0 miRNAWalker2 validate -1.19 0 NA
8 hsa-miR-30c-5p RRM2 -1.09 0 2.68 0 miRNAWalker2 validate -0.88 0 NA
9 hsa-miR-362-3p RRM2 -0.75 0 2.68 0 miRanda -0.35 2.0E-5 NA
10 hsa-miR-429 RRM2 -2.17 0 2.68 0 miRanda -0.61 0 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 NUCLEOBASE CONTAINING SMALL MOLECULE METABOLIC PROCESS 18 535 3.071e-15 1.429e-11
2 ORGANOPHOSPHATE METABOLIC PROCESS 20 885 1.164e-13 2.708e-10
3 PURINE CONTAINING COMPOUND METABOLIC PROCESS 14 394 2.887e-12 4.478e-09
4 NUCLEOSIDE PHOSPHATE BIOSYNTHETIC PROCESS 11 188 3.888e-12 4.523e-09
5 PHOSPHATE CONTAINING COMPOUND METABOLIC PROCESS 24 1977 1.25e-10 1.163e-07
6 PURINE CONTAINING COMPOUND BIOSYNTHETIC PROCESS 9 139 1.673e-10 1.297e-07
7 ORGANOPHOSPHATE BIOSYNTHETIC PROCESS 13 450 2.5e-10 1.662e-07
8 CYCLIC NUCLEOTIDE BIOSYNTHETIC PROCESS 6 34 4.63e-10 2.693e-07
9 SMALL MOLECULE METABOLIC PROCESS 22 1767 6.461e-10 3.34e-07
10 CAMP BIOSYNTHETIC PROCESS 5 17 8.645e-10 4.022e-07
11 CYCLIC NUCLEOTIDE METABOLIC PROCESS 6 57 1.189e-08 5.029e-06
12 RENAL SYSTEM PROCESS 7 102 1.377e-08 5.338e-06
13 RENAL WATER HOMEOSTASIS 5 34 3.749e-08 1.246e-05
14 CAMP METABOLIC PROCESS 5 34 3.749e-08 1.246e-05
15 WATER HOMEOSTASIS 6 70 4.178e-08 1.296e-05
16 CAMP MEDIATED SIGNALING 5 37 5.836e-08 1.697e-05
17 ACTIVATION OF PROTEIN KINASE A ACTIVITY 4 17 1.277e-07 3.494e-05
18 CYCLIC NUCLEOTIDE MEDIATED SIGNALING 5 46 1.8e-07 4.654e-05
19 MULTICELLULAR ORGANISMAL WATER HOMEOSTASIS 5 58 5.867e-07 0.0001437
20 CARBOHYDRATE DERIVATIVE METABOLIC PROCESS 14 1047 7.845e-07 0.0001825
21 MULTICELLULAR ORGANISMAL HOMEOSTASIS 8 272 8.526e-07 0.0001889
22 ADENYLATE CYCLASE INHIBITING G PROTEIN COUPLED RECEPTOR SIGNALING PATHWAY 5 68 1.307e-06 0.0002763
23 ADENYLATE CYCLASE ACTIVATING G PROTEIN COUPLED RECEPTOR SIGNALING PATHWAY 5 73 1.863e-06 0.0003769
24 SINGLE ORGANISM BIOSYNTHETIC PROCESS 15 1340 2.711e-06 0.0005257
25 NUCLEOSIDE DIPHOSPHATE METABOLIC PROCESS 5 84 3.74e-06 0.0006783
26 CELLULAR RESPONSE TO GLUCAGON STIMULUS 4 38 3.79e-06 0.0006783
27 ACTIVATION OF ADENYLATE CYCLASE ACTIVITY 4 39 4.214e-06 0.0007263
28 ORGANONITROGEN COMPOUND METABOLIC PROCESS 17 1796 4.868e-06 0.000809
29 OXIDATION REDUCTION PROCESS 12 898 5.61e-06 0.0008971
30 RESPONSE TO OXIDATIVE STRESS 8 352 5.784e-06 0.0008971
31 GUANOSINE CONTAINING COMPOUND METABOLIC PROCESS 4 46 8.241e-06 0.001237
32 POSITIVE REGULATION OF ADENYLATE CYCLASE ACTIVITY 4 48 9.785e-06 0.00138
33 RESPONSE TO GLUCAGON 4 48 9.785e-06 0.00138
34 RESPONSE TO REACTIVE OXYGEN SPECIES 6 191 1.531e-05 0.002095
35 ORGANONITROGEN COMPOUND BIOSYNTHETIC PROCESS 12 1024 2.101e-05 0.002793
36 GMP METABOLIC PROCESS 3 20 2.292e-05 0.002962
37 POSITIVE REGULATION OF LYASE ACTIVITY 4 61 2.554e-05 0.003128
38 POSITIVE REGULATION OF CYCLASE ACTIVITY 4 61 2.554e-05 0.003128
39 POSITIVE REGULATION OF PURINE NUCLEOTIDE METABOLIC PROCESS 5 133 3.509e-05 0.004082
40 POSITIVE REGULATION OF NUCLEOTIDE METABOLIC PROCESS 5 133 3.509e-05 0.004082
41 REGULATION OF ADENYLATE CYCLASE ACTIVITY 4 70 4.405e-05 0.004999
42 ADENYLATE CYCLASE MODULATING G PROTEIN COUPLED RECEPTOR SIGNALING PATHWAY 5 145 5.303e-05 0.005831
43 NUCLEOSIDE MONOPHOSPHATE METABOLIC PROCESS 6 239 5.388e-05 0.005831
44 ORGANIC HYDROXY COMPOUND TRANSPORT 5 155 7.279e-05 0.007526
45 GLYCOSYL COMPOUND METABOLIC PROCESS 7 368 7.203e-05 0.007526
46 SECOND MESSENGER MEDIATED SIGNALING 5 160 8.459e-05 0.008556
47 COENZYME METABOLIC PROCESS 6 265 9.529e-05 0.009434
48 REGULATION OF LYASE ACTIVITY 4 86 9.869e-05 0.009567
NumGOOverlapSizeP ValueAdj. P Value
1 CYCLASE ACTIVITY 5 22 3.64e-09 3.382e-06
2 ADENYL NUCLEOTIDE BINDING 17 1514 4.592e-07 0.0002133
3 RIBONUCLEOTIDE BINDING 18 1860 1.684e-06 0.0005215
4 OXIDOREDUCTASE ACTIVITY 11 719 4.086e-06 0.000949
5 PROTEIN PHOSPHATASE BINDING 5 120 2.139e-05 0.003174
6 ORGANIC HYDROXY COMPOUND TRANSMEMBRANE TRANSPORTER ACTIVITY 4 60 2.392e-05 0.003174
7 LIGASE ACTIVITY FORMING CARBON NITROGEN BONDS 4 56 1.817e-05 0.003174
8 ADENYLYLTRANSFERASE ACTIVITY 3 24 4.036e-05 0.004687
9 PHOSPHATASE BINDING 5 162 8.97e-05 0.009259
NumGOOverlapSizeP ValueAdj. P Value
1 OXIDOREDUCTASE COMPLEX 5 93 6.177e-06 0.003608

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 hsa00230_Purine_metabolism 7 162 3.338e-07 6.009e-05
2 hsa04976_Bile_secretion 5 71 1.622e-06 0.0001459
3 hsa04971_Gastric_acid_secretion 4 74 5.482e-05 0.003289
4 hsa04914_Progesterone.mediated_oocyte_maturation 4 87 0.0001032 0.003533
5 hsa04970_Salivary_secretion 4 89 0.0001128 0.003533
6 hsa04540_Gap_junction 4 90 0.0001178 0.003533
7 hsa04912_GnRH_signaling_pathway 4 101 0.0001839 0.003679
8 hsa04916_Melanogenesis 4 101 0.0001839 0.003679
9 hsa04972_Pancreatic_secretion 4 101 0.0001839 0.003679
10 hsa00310_Lysine_degradation 3 44 0.0002538 0.004569
11 hsa04114_Oocyte_meiosis 4 114 0.0002926 0.00469
12 hsa04270_Vascular_smooth_muscle_contraction 4 116 0.0003127 0.00469
13 hsa04062_Chemokine_signaling_pathway 4 189 0.001934 0.02678
14 hsa00240_Pyrimidine_metabolism 3 99 0.002697 0.03467
15 hsa00020_Citrate_cycle_.TCA_cycle. 2 30 0.003185 0.03822
16 hsa00640_Propanoate_metabolism 2 32 0.003619 0.04071
17 hsa00620_Pyruvate_metabolism 2 40 0.00561 0.0594
18 hsa00380_Tryptophan_metabolism 2 42 0.006171 0.06171
19 hsa04962_Vasopressin.regulated_water_reabsorption 2 44 0.006756 0.064
20 hsa04742_Taste_transduction 2 52 0.009335 0.08401
21 hsa04020_Calcium_signaling_pathway 3 177 0.0134 0.1149
22 hsa04520_Adherens_junction 2 73 0.01782 0.1395
23 hsa04910_Insulin_signaling_pathway 2 138 0.05715 0.381
24 hsa04390_Hippo_signaling_pathway 2 154 0.06926 0.3957
25 hsa04141_Protein_processing_in_endoplasmic_reticulum 2 168 0.08048 0.4261
26 hsa04510_Focal_adhesion 2 200 0.108 0.534
27 hsa04010_MAPK_signaling_pathway 2 268 0.1728 0.6557
28 hsa04151_PI3K_AKT_signaling_pathway 2 351 0.2578 0.8594

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 RP11-196G18.22 hsa-let-7e-5p;hsa-let-7g-5p;hsa-miR-125a-5p;hsa-miR-199a-5p;hsa-miR-20b-5p;hsa-miR-26a-5p;hsa-miR-30a-5p;hsa-miR-30c-5p;hsa-miR-362-3p;hsa-miR-429 10 RRM2 Sponge network 1.285 0 2.684 0 0.5

Quest ID: 2bb3e7731dbdc60519557b55a12a6995