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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-29a-3p RALA -0.7 0 0.19 0.00013 miRNATAP -0.1 0 NA
2 hsa-miR-29c-3p RALA -0.07 0.56377 0.19 0.00013 miRNATAP -0.15 0 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 REGULATION OF GTPASE ACTIVITY 69 673 9.256e-23 4.307e-19
2 POSITIVE REGULATION OF HYDROLASE ACTIVITY 74 905 1.325e-18 3.082e-15
3 POSITIVE REGULATION OF CATALYTIC ACTIVITY 100 1518 2.659e-18 4.124e-15
4 INTRACELLULAR SIGNAL TRANSDUCTION 101 1572 9.793e-18 1.139e-14
5 POSITIVE REGULATION OF MOLECULAR FUNCTION 106 1791 4.079e-16 3.795e-13
6 REGULATION OF HYDROLASE ACTIVITY 87 1327 8.546e-16 6.628e-13
7 SMALL GTPASE MEDIATED SIGNAL TRANSDUCTION 38 352 1.176e-13 7.814e-11
8 PHOSPHATE CONTAINING COMPOUND METABOLIC PROCESS 101 1977 2.103e-11 1.223e-08
9 PROTEIN PHOSPHORYLATION 61 944 5.221e-11 2.699e-08
10 INTRACELLULAR PROTEIN TRANSPORT 54 781 6.2e-11 2.885e-08
11 ACTIVATION OF GTPASE ACTIVITY 16 75 7.213e-11 3.051e-08
12 REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION 84 1656 2.043e-09 7.922e-07
13 REGULATION OF SMALL GTPASE MEDIATED SIGNAL TRANSDUCTION 27 278 4.67e-09 1.671e-06
14 REGULATION OF VESICLE FUSION 13 62 5.546e-09 1.843e-06
15 PHOSPHORYLATION 67 1228 6.707e-09 2.08e-06
16 REGULATION OF PHOSPHORUS METABOLIC PROCESS 80 1618 1.647e-08 4.791e-06
17 CELLULAR MACROMOLECULE LOCALIZATION 66 1234 1.906e-08 5.218e-06
18 PROTEIN LOCALIZATION 86 1805 2.4e-08 6.204e-06
19 REGULATION OF KINASE ACTIVITY 48 776 2.713e-08 6.644e-06
20 PROTEIN AUTOPHOSPHORYLATION 21 192 3.154e-08 7.338e-06
21 RAS PROTEIN SIGNAL TRANSDUCTION 18 143 3.492e-08 7.737e-06
22 REGULATION OF ARF PROTEIN SIGNAL TRANSDUCTION 7 16 7.202e-08 1.523e-05
23 PEPTIDYL TYROSINE MODIFICATION 20 186 8.917e-08 1.729e-05
24 ACTIVATION OF PROTEIN KINASE ACTIVITY 25 279 8.557e-08 1.729e-05
25 ACTIVATION OF PROTEIN KINASE A ACTIVITY 7 17 1.197e-07 2.228e-05
26 POSITIVE REGULATION OF PHOSPHATE METABOLIC PROCESS 56 1036 1.788e-07 2.894e-05
27 ESTABLISHMENT OF PROTEIN LOCALIZATION 70 1423 1.797e-07 2.894e-05
28 REGULATION OF VESICLE MEDIATED TRANSPORT 33 462 1.804e-07 2.894e-05
29 POSITIVE REGULATION OF PHOSPHORUS METABOLIC PROCESS 56 1036 1.788e-07 2.894e-05
30 POSITIVE REGULATION OF BIOSYNTHETIC PROCESS 83 1805 2.035e-07 3.154e-05
31 REGULATION OF CELL PROJECTION ORGANIZATION 37 558 2.101e-07 3.154e-05
32 CAMP MEDIATED SIGNALING 9 37 3.295e-07 4.792e-05
33 REGULATION OF PROTEIN MODIFICATION PROCESS 79 1710 3.493e-07 4.832e-05
34 REGULATION OF RAS PROTEIN SIGNAL TRANSDUCTION 19 184 3.531e-07 4.832e-05
35 RENAL SYSTEM PROCESS 14 102 3.963e-07 5.269e-05
36 REGULATION OF MULTICELLULAR ORGANISMAL DEVELOPMENT 77 1672 5.702e-07 7.37e-05
37 SIGNAL TRANSDUCTION BY PROTEIN PHOSPHORYLATION 29 404 9.141e-07 0.000115
38 REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 80 1784 9.589e-07 0.0001174
39 ESTABLISHMENT OF LOCALIZATION IN CELL 76 1676 1.232e-06 0.000147
40 NEGATIVE REGULATION OF PHOSPHORYLATION 29 422 2.192e-06 0.0002549
41 CYCLIC NUCLEOTIDE MEDIATED SIGNALING 9 46 2.37e-06 0.000269
42 CAMP BIOSYNTHETIC PROCESS 6 17 2.91e-06 0.0003224
43 POSITIVE REGULATION OF CYCLASE ACTIVITY 10 61 3.551e-06 0.0003843
44 REGULATION OF TRANSFERASE ACTIVITY 49 946 3.649e-06 0.0003859
45 REGULATION OF MAPK CASCADE 38 660 4.449e-06 0.00046
46 CELLULAR RESPONSE TO GLUCAGON STIMULUS 8 38 4.868e-06 0.0004819
47 NEGATIVE REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 41 740 4.768e-06 0.0004819
48 NEGATIVE REGULATION OF PHOSPHORUS METABOLIC PROCESS 33 541 5.827e-06 0.0005427
49 REGULATION OF CILIUM ASSEMBLY 9 51 5.832e-06 0.0005427
50 NEGATIVE REGULATION OF PHOSPHATE METABOLIC PROCESS 33 541 5.827e-06 0.0005427
51 REGULATION OF TRANSPORT 77 1804 9.693e-06 0.0008843
52 POSITIVE REGULATION OF KINASE ACTIVITY 30 482 1.052e-05 0.0009411
53 INOSITOL PHOSPHATE METABOLIC PROCESS 9 56 1.294e-05 0.001117
54 REGULATION OF CYCLIC NUCLEOTIDE METABOLIC PROCESS 15 155 1.323e-05 0.001117
55 POSITIVE REGULATION OF PROTEIN MODIFICATION PROCESS 54 1135 1.344e-05 0.001117
56 REGULATION OF CELL PROJECTION ASSEMBLY 15 155 1.323e-05 0.001117
57 REGULATION OF STRESS ACTIVATED PROTEIN KINASE SIGNALING CASCADE 17 197 1.641e-05 0.00134
58 ACTIN FILAMENT BASED PROCESS 28 450 2.079e-05 0.001639
59 PHOSPHATIDYLINOSITOL DEPHOSPHORYLATION 6 23 2.079e-05 0.001639
60 RENAL WATER HOMEOSTASIS 7 34 2.256e-05 0.001693
61 CYCLIC NUCLEOTIDE BIOSYNTHETIC PROCESS 7 34 2.256e-05 0.001693
62 CAMP METABOLIC PROCESS 7 34 2.256e-05 0.001693
63 POSITIVE REGULATION OF LYASE ACTIVITY 9 61 2.64e-05 0.001943
64 POSITIVE REGULATION OF CYCLIC NUCLEOTIDE METABOLIC PROCESS 12 109 2.673e-05 0.001943
65 ACTIVATION OF JUN KINASE ACTIVITY 7 35 2.757e-05 0.001953
66 NEUROGENESIS 62 1402 2.813e-05 0.001953
67 POSITIVE REGULATION OF PROTEIN METABOLIC PROCESS 65 1492 2.805e-05 0.001953
68 POSITIVE REGULATION OF ADENYLATE CYCLASE ACTIVITY 8 48 2.99e-05 0.002016
69 RESPONSE TO GLUCAGON 8 48 2.99e-05 0.002016
70 REGULATION OF CAMP METABOLIC PROCESS 13 129 3.223e-05 0.002142
71 CELLULAR RESPONSE TO PEPTIDE 20 274 3.542e-05 0.002321
72 CELLULAR RESPONSE TO ENDOGENOUS STIMULUS 48 1008 4.06e-05 0.002624
73 NEURON PROJECTION DEVELOPMENT 31 545 4.281e-05 0.002729
74 NEGATIVE REGULATION OF NITROGEN COMPOUND METABOLIC PROCESS 65 1517 4.635e-05 0.002914
75 POSITIVE REGULATION OF GENE EXPRESSION 72 1733 4.718e-05 0.002927
76 CELL PROJECTION ORGANIZATION 44 902 4.923e-05 0.003014
77 POSITIVE REGULATION OF STRESS ACTIVATED PROTEIN KINASE SIGNALING CASCADE 13 135 5.2e-05 0.003102
78 JNK CASCADE 10 82 5.174e-05 0.003102
79 REGULATION OF ANATOMICAL STRUCTURE MORPHOGENESIS 48 1021 5.567e-05 0.003279
80 ACTIVATION OF ADENYLATE CYCLASE ACTIVITY 7 39 5.764e-05 0.003313
81 NEURON PROJECTION MORPHOGENESIS 25 402 5.768e-05 0.003313
82 ACTIVATION OF MAPK ACTIVITY 13 137 6.06e-05 0.003439
83 RESPONSE TO PEPTIDE 25 404 6.247e-05 0.00346
84 REGULATION OF CELLULAR COMPONENT MOVEMENT 39 771 6.188e-05 0.00346
85 REGULATION OF CELLULAR RESPONSE TO STRESS 36 691 6.574e-05 0.003599
86 NEGATIVE REGULATION OF SMALL GTPASE MEDIATED SIGNAL TRANSDUCTION 7 40 6.832e-05 0.003696
87 PHOSPHATIDYLINOSITOL BIOSYNTHETIC PROCESS 12 120 6.949e-05 0.003717
88 VESICLE MEDIATED TRANSPORT 55 1239 7.438e-05 0.003889
89 POSITIVE REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 47 1004 7.384e-05 0.003889
90 EMBRYO DEVELOPMENT 43 894 8.254e-05 0.004267
91 TISSUE DEVELOPMENT 64 1518 8.531e-05 0.004362
92 REGULATION OF MAP KINASE ACTIVITY 21 319 0.0001012 0.005116
93 NEGATIVE REGULATION OF KINASE ACTIVITY 18 250 0.0001026 0.005131
94 POSITIVE REGULATION OF CAMP METABOLIC PROCESS 10 89 0.0001046 0.005145
95 CELL MORPHOGENESIS INVOLVED IN NEURON DIFFERENTIATION 23 368 0.0001051 0.005145
96 CYCLIC NUCLEOTIDE METABOLIC PROCESS 8 57 0.0001067 0.005171
97 POSITIVE REGULATION OF MAPK CASCADE 27 470 0.0001125 0.005398
98 NEURON DEVELOPMENT 35 687 0.0001283 0.006091
99 CELLULAR RESPONSE TO OXYGEN CONTAINING COMPOUND 39 799 0.0001309 0.006153
100 REGULATION OF NUCLEOTIDE METABOLIC PROCESS 16 211 0.0001355 0.006305
101 ORGANOPHOSPHATE BIOSYNTHETIC PROCESS 26 450 0.000137 0.006311
102 CELL DEVELOPMENT 60 1426 0.0001524 0.00695
103 PHOSPHATIDYLINOSITOL METABOLIC PROCESS 15 193 0.0001661 0.007504
104 NEGATIVE REGULATION OF GENE EXPRESSION 62 1493 0.0001685 0.00754
105 REGULATION OF ERK1 AND ERK2 CASCADE 17 238 0.0001744 0.007697
106 POSITIVE REGULATION OF TRANSFERASE ACTIVITY 32 616 0.0001753 0.007697
107 REGULATION OF CELL PROLIFERATION 62 1496 0.000178 0.007741
108 POSITIVE REGULATION OF PURINE NUCLEOTIDE METABOLIC PROCESS 12 133 0.0001865 0.007956
109 POSITIVE REGULATION OF NUCLEOTIDE METABOLIC PROCESS 12 133 0.0001865 0.007956
110 REGULATION OF NEURON PROJECTION DEVELOPMENT 24 408 0.0001881 0.007956
111 DEPHOSPHORYLATION 19 286 0.0001903 0.007978
112 POSITIVE REGULATION OF CELL COMMUNICATION 63 1532 0.0001948 0.008094
113 NEGATIVE REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION 25 437 0.0002132 0.008781
114 PHOSPHOLIPID DEPHOSPHORYLATION 6 34 0.0002173 0.00883
115 POSITIVE REGULATION OF JUN KINASE ACTIVITY 8 63 0.0002182 0.00883
116 REGULATION OF CELLULAR COMPONENT BIOGENESIS 37 767 0.0002445 0.009807
NumGOOverlapSizeP ValueAdj. P Value
1 RIBONUCLEOTIDE BINDING 115 1860 5.678e-19 5.275e-16
2 MOLECULAR FUNCTION REGULATOR 89 1353 3.053e-16 1.418e-13
3 NUCLEIC ACID BINDING TRANSCRIPTION FACTOR ACTIVITY 81 1199 1.89e-15 5.851e-13
4 NUCLEOSIDE TRIPHOSPHATASE REGULATOR ACTIVITY 36 329 3.54e-13 8.222e-11
5 ADENYL NUCLEOTIDE BINDING 88 1514 5.995e-13 1.114e-10
6 PROTEIN KINASE ACTIVITY 49 640 1.476e-11 2.285e-09
7 ENZYME ACTIVATOR ACTIVITY 39 471 2.044e-10 2.712e-08
8 KINASE ACTIVITY 55 842 3.4e-10 3.949e-08
9 GTPASE ACTIVITY 26 246 1.51e-09 1.558e-07
10 GUANYL NUCLEOTIDE EXCHANGE FACTOR ACTIVITY 28 303 7.289e-09 6.156e-07
11 PROTEIN SERINE THREONINE KINASE ACTIVITY 35 445 6.794e-09 6.156e-07
12 GTPASE BINDING 27 295 1.662e-08 1.223e-06
13 TRANSFERASE ACTIVITY TRANSFERRING PHOSPHORUS CONTAINING GROUPS 57 992 1.711e-08 1.223e-06
14 MOTOR ACTIVITY 17 131 5.314e-08 3.526e-06
15 ENZYME REGULATOR ACTIVITY 54 959 8.154e-08 5.05e-06
16 RECEPTOR SIGNALING PROTEIN SERINE THREONINE KINASE ACTIVITY 14 92 1.065e-07 6.184e-06
17 RECEPTOR SIGNALING PROTEIN ACTIVITY 19 172 1.22e-07 6.664e-06
18 GUANYL NUCLEOTIDE BINDING 30 390 1.35e-07 6.968e-06
19 HYDROLASE ACTIVITY ACTING ON ACID ANHYDRIDES 48 820 1.442e-07 7.048e-06
20 REGULATORY REGION NUCLEIC ACID BINDING 47 818 3.352e-07 1.557e-05
21 PHOSPHATIDYLINOSITOL PHOSPHATE 5 PHOSPHATASE ACTIVITY 6 13 4.41e-07 1.951e-05
22 RAB GTPASE BINDING 15 120 5.288e-07 2.233e-05
23 ENZYME BINDING 79 1737 6.523e-07 2.635e-05
24 PROTEIN TYROSINE KINASE ACTIVITY 18 176 8.257e-07 3.196e-05
25 CYCLASE ACTIVITY 7 22 9.374e-07 3.428e-05
26 SEQUENCE SPECIFIC DNA BINDING 54 1037 9.593e-07 3.428e-05
27 DOUBLE STRANDED DNA BINDING 43 764 1.856e-06 6.16e-05
28 ARF GUANYL NUCLEOTIDE EXCHANGE FACTOR ACTIVITY 7 24 1.818e-06 6.16e-05
29 RNA POLYMERASE II TRANSCRIPTION FACTOR ACTIVITY SEQUENCE SPECIFIC DNA BINDING 37 629 3.659e-06 0.0001172
30 CYTOSKELETAL PROTEIN BINDING 44 819 4.683e-06 0.0001373
31 INOSITOL TETRAKISPHOSPHATE PHOSPHATASE ACTIVITY 5 11 4.73e-06 0.0001373
32 INOSITOL TRISPHOSPHATE PHOSPHATASE ACTIVITY 5 11 4.73e-06 0.0001373
33 INOSITOL PHOSPHATE PHOSPHATASE ACTIVITY 6 20 8.529e-06 0.0002401
34 SH3 DOMAIN BINDING 13 116 1.023e-05 0.0002796
35 KINASE BINDING 34 606 2.425e-05 0.0006437
36 MICROTUBULE MOTOR ACTIVITY 10 77 2.979e-05 0.0007688
37 ATP DEPENDENT MICROTUBULE MOTOR ACTIVITY 5 18 7.543e-05 0.001894
38 PHOSPHATIDYLINOSITOL PHOSPHATE PHOSPHATASE ACTIVITY 6 29 8.567e-05 0.002094
39 POTASSIUM CHANNEL REGULATOR ACTIVITY 7 46 0.0001714 0.004084
40 PROTEIN DOMAIN SPECIFIC BINDING 32 624 0.0002208 0.005128
41 PHOSPHORIC ESTER HYDROLASE ACTIVITY 22 368 0.0002756 0.006244
42 CORE PROMOTER PROXIMAL REGION DNA BINDING 22 371 0.0003083 0.006819
43 RAS GUANYL NUCLEOTIDE EXCHANGE FACTOR ACTIVITY 16 228 0.0003272 0.007037
44 PHOSPHATASE ACTIVITY 18 275 0.0003333 0.007037
45 MAP KINASE ACTIVITY 4 14 0.0003674 0.007586
46 SNAP RECEPTOR ACTIVITY 6 38 0.0004084 0.008249
NumGOOverlapSizeP ValueAdj. P Value
1 KINESIN COMPLEX 10 55 1.324e-06 0.0002578
2 NEURON PART 63 1265 5.219e-07 0.0002578
3 CELL PROJECTION 80 1786 1.002e-06 0.0002578
4 CELL LEADING EDGE 25 350 5.629e-06 0.0008219
5 CELL PROJECTION PART 48 946 7.986e-06 0.0009327
6 NEURON PROJECTION 47 942 1.534e-05 0.001493
7 CYTOPLASMIC SIDE OF MEMBRANE 15 170 3.949e-05 0.003295
8 PRESYNAPSE 20 283 5.577e-05 0.004072

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 Rap1_signaling_pathway_hsa04015 24 206 9.088e-10 4.726e-08
2 Endocytosis_hsa04144 24 244 2.645e-08 6.841e-07
3 Phospholipase_D_signaling_pathway_hsa04072 18 146 4.836e-08 6.841e-07
4 Gap_junction_hsa04540 14 88 5.98e-08 6.841e-07
5 MAPK_signaling_pathway_hsa04010 26 295 6.578e-08 6.841e-07
6 Ras_signaling_pathway_hsa04014 21 232 7.843e-07 6.797e-06
7 cAMP_signaling_pathway_hsa04024 18 198 4.504e-06 3.346e-05
8 cGMP_PKG_signaling_pathway_hsa04022 15 163 2.412e-05 0.0001568
9 Apelin_signaling_pathway_hsa04371 13 137 6.06e-05 0.0003398
10 Apoptosis_hsa04210 13 138 6.535e-05 0.0003398
11 TNF_signaling_pathway_hsa04668 11 108 0.0001173 0.0005545
12 PI3K_Akt_signaling_pathway_hsa04151 22 352 0.0001476 0.0006396
13 mTOR_signaling_pathway_hsa04150 13 151 0.0001634 0.0006453
14 FoxO_signaling_pathway_hsa04068 12 132 0.0001737 0.0006453
15 Signaling_pathways_regulating_pluripotency_of_stem_cells_hsa04550 11 139 0.001035 0.003587
16 Phosphatidylinositol_signaling_system_hsa04070 9 99 0.001104 0.003588
17 Tight_junction_hsa04530 12 170 0.001679 0.005137
18 Autophagy_animal_hsa04140 10 128 0.001901 0.005492
19 Focal_adhesion_hsa04510 13 199 0.002192 0.006
20 Calcium_signaling_pathway_hsa04020 12 182 0.002961 0.007699
21 AMPK_signaling_pathway_hsa04152 9 121 0.004373 0.01083
22 Oocyte_meiosis_hsa04114 9 124 0.005132 0.01213
23 ErbB_signaling_pathway_hsa04012 7 85 0.006647 0.01503
24 Regulation_of_actin_cytoskeleton_hsa04810 12 208 0.008456 0.01832
25 HIF_1_signaling_pathway_hsa04066 7 100 0.01551 0.03226
26 Sphingolipid_signaling_pathway_hsa04071 7 118 0.03453 0.06907
27 VEGF_signaling_pathway_hsa04370 4 59 0.06718 0.1294
28 Hedgehog_signaling_pathway_hsa04340 3 47 0.1228 0.223
29 Cellular_senescence_hsa04218 7 160 0.1244 0.223
30 Notch_signaling_pathway_hsa04330 3 48 0.1286 0.223
31 Apoptosis_multiple_species_hsa04215 2 33 0.2114 0.3458
32 Hippo_signaling_pathway_hsa04390 6 154 0.2128 0.3458
33 Mitophagy_animal_hsa04137 3 65 0.2389 0.3764
34 Adherens_junction_hsa04520 3 72 0.2882 0.4407
35 ABC_transporters_hsa02010 2 45 0.3274 0.4864
36 Lysosome_hsa04142 4 123 0.3977 0.5745
37 NF_kappa_B_signaling_pathway_hsa04064 3 95 0.4503 0.6329
38 Wnt_signaling_pathway_hsa04310 4 146 0.5284 0.7126
39 Jak_STAT_signaling_pathway_hsa04630 4 162 0.6107 0.7531
40 Necroptosis_hsa04217 4 164 0.6203 0.7531
41 ECM_receptor_interaction_hsa04512 2 82 0.6329 0.7531
42 Peroxisome_hsa04146 2 83 0.6395 0.7531
43 Phagosome_hsa04145 3 152 0.7597 0.8588
44 Cell_adhesion_molecules_.CAMs._hsa04514 2 145 0.894 0.9488
45 Neuroactive_ligand_receptor_interaction_hsa04080 3 278 0.977 0.9936
46 Cytokine_cytokine_receptor_interaction_hsa04060 2 270 0.9936 0.9936

Quest ID: eab2a319fba49ca57243423cb74c01f2