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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-15a-5p BMI1 -0.74 0.01074 -0.18 0.45133 miRNAWalker2 validate; miRTarBase -0.14 0.0172 27596816 Our results suggest that overexpression of miR-15a and miR-16 mediates down-regulation of BMI1 and leads to mitochondrial mediated apoptosis
2 hsa-miR-362-3p BMI1 -1.21 0.01257 -0.18 0.45133 miRanda -0.11 0.00173 NA
3 hsa-miR-455-5p BMI1 -0.23 0.54044 -0.18 0.45133 miRanda -0.11 0.01889 NA
4 hsa-miR-590-3p BMI1 -0.92 0.03456 -0.18 0.45133 miRanda; mirMAP -0.12 0.00201 NA
NumGOOverlapSizeP ValueAdj. P Value
1 CHROMOSOME ORGANIZATION 20 1009 5.404e-10 2.515e-06
2 INTERSPECIES INTERACTION BETWEEN ORGANISMS 16 662 2.412e-09 3.741e-06
3 SYMBIOSIS ENCOMPASSING MUTUALISM THROUGH PARASITISM 16 662 2.412e-09 3.741e-06
4 CELL SEPARATION AFTER CYTOKINESIS 5 17 3.869e-09 4.501e-06
5 RNA PROCESSING 17 835 9.218e-09 8.579e-06
6 VIRAL BUDDING 5 24 2.604e-08 1.514e-05
7 MULTI ORGANISM ORGANELLE ORGANIZATION 5 24 2.604e-08 1.514e-05
8 MULTI ORGANISM MEMBRANE BUDDING 5 24 2.604e-08 1.514e-05
9 CHROMOSOME LOCALIZATION 6 61 1.07e-07 4.147e-05
10 MULTIVESICULAR BODY ORGANIZATION 5 31 1.02e-07 4.147e-05
11 MITOTIC NUCLEAR DIVISION 11 361 9.931e-08 4.147e-05
12 MULTI ORGANISM MEMBRANE ORGANIZATION 5 31 1.02e-07 4.147e-05
13 CELL DIVISION 12 460 1.336e-07 4.783e-05
14 VIRION ASSEMBLY 5 37 2.571e-07 7.476e-05
15 CELL CYCLE 19 1316 2.564e-07 7.476e-05
16 REGULATION OF ORGANELLE ORGANIZATION 18 1178 2.479e-07 7.476e-05
17 CELL CYCLE PROCESS 17 1081 3.832e-07 0.0001049
18 METAPHASE PLATE CONGRESSION 5 42 4.944e-07 0.0001278
19 MITOTIC CELL CYCLE 14 766 8.323e-07 0.0002038
20 POSITIVE REGULATION OF VIRAL PROCESS 6 92 1.253e-06 0.0002916
21 VIRAL LIFE CYCLE 9 290 1.361e-06 0.0003015
22 REGULATION OF CELLULAR RESPONSE TO STRESS 13 691 1.572e-06 0.0003325
23 ORGANELLE FISSION 11 496 2.286e-06 0.0004624
24 MRNA METABOLIC PROCESS 12 611 2.674e-06 0.0005184
25 PROTEIN K11 LINKED UBIQUITINATION 4 27 2.998e-06 0.000558
26 REGULATION OF PROTEIN MODIFICATION PROCESS 20 1710 3.191e-06 0.0005711
27 ENDOSOME ORGANIZATION 5 62 3.548e-06 0.0006115
28 DNA METABOLIC PROCESS 13 758 4.341e-06 0.0007214
29 POSITIVE REGULATION OF CELLULAR COMPONENT ORGANIZATION 16 1152 4.511e-06 0.0007237
30 RRNA METABOLIC PROCESS 8 255 5.051e-06 0.0007835
31 REGULATION OF VIRAL RELEASE FROM HOST CELL 4 31 5.315e-06 0.0007977
32 RNA SPLICING VIA TRANSESTERIFICATION REACTIONS 8 267 7.076e-06 0.001029
33 MACROMOLECULE CATABOLIC PROCESS 14 926 7.569e-06 0.001067
34 ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE 9 361 8.099e-06 0.001108
35 POSITIVE REGULATION OF ORGANELLE ORGANIZATION 11 573 9.026e-06 0.001195
36 RNA SPLICING 9 367 9.243e-06 0.001195
37 REGULATION OF CELL CYCLE 14 949 9.998e-06 0.001257
38 EXIT FROM MITOSIS 3 12 1.088e-05 0.001332
39 REGULATION OF SYMBIOSIS ENCOMPASSING MUTUALISM THROUGH PARASITISM 7 205 1.181e-05 0.001409
40 NUCLEUS ORGANIZATION 6 136 1.213e-05 0.001411
41 NCRNA PROCESSING 9 386 1.382e-05 0.001569
42 POSITIVE REGULATION OF PROTEIN MODIFICATION PROCESS 15 1135 1.704e-05 0.001888
43 RIBOSOME BIOGENESIS 8 308 1.991e-05 0.002155
44 REGULATION OF TELOMERASE RNA LOCALIZATION TO CAJAL BODY 3 15 2.231e-05 0.002209
45 POSITIVE REGULATION OF VIRAL RELEASE FROM HOST CELL 3 15 2.231e-05 0.002209
46 POSITIVE REGULATION OF TELOMERASE RNA LOCALIZATION TO CAJAL BODY 3 15 2.231e-05 0.002209
47 REGULATION OF SPINDLE ASSEMBLY 3 15 2.231e-05 0.002209
48 MITOTIC SISTER CHROMATID SEGREGATION 5 91 2.343e-05 0.002227
49 NUCLEAR CHROMOSOME SEGREGATION 7 228 2.345e-05 0.002227
50 REGULATION OF CELL DEATH 17 1472 2.448e-05 0.002278
51 SINGLE ORGANISM CELLULAR LOCALIZATION 13 898 2.642e-05 0.00241
52 POSITIVE REGULATION OF MULTI ORGANISM PROCESS 6 157 2.739e-05 0.002451
53 POSITIVE REGULATION OF PROTEIN METABOLIC PROCESS 17 1492 2.91e-05 0.002554
54 REGULATION OF NUCLEAR DIVISION 6 163 3.382e-05 0.002861
55 MRNA PROCESSING 9 432 3.352e-05 0.002861
56 CHROMATIN ORGANIZATION 11 663 3.481e-05 0.002892
57 PROTEIN COMPLEX SUBUNIT ORGANIZATION 17 1527 3.907e-05 0.003189
58 VACUOLE ORGANIZATION 6 168 4.006e-05 0.003214
59 PROTEIN LOCALIZATION TO ORGANELLE 10 556 4.159e-05 0.00328
60 REGULATION OF CELL CYCLE PROCESS 10 558 4.287e-05 0.003325
61 ESTABLISHMENT OF PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM 5 104 4.462e-05 0.0034
62 REGULATION OF TRANSFERASE ACTIVITY 13 946 4.53e-05 0.0034
63 CELL CYCLE PHASE TRANSITION 7 255 4.785e-05 0.003534
64 SISTER CHROMATID SEGREGATION 6 176 5.193e-05 0.003776
65 REGULATION OF SPINDLE ORGANIZATION 3 20 5.515e-05 0.003948
66 PROTEIN CATABOLIC PROCESS 10 579 5.843e-05 0.004058
67 POSITIVE REGULATION OF LIGASE ACTIVITY 5 110 5.836e-05 0.004058
68 ESTABLISHMENT OF PROTEIN LOCALIZATION TO MEMBRANE 7 264 5.956e-05 0.004075
69 REGULATION OF MITOTIC CELL CYCLE 9 468 6.226e-05 0.004198
70 CHROMOSOME SEGREGATION 7 272 7.185e-05 0.004597
71 NEGATIVE REGULATION OF ORGANELLE ASSEMBLY 3 22 7.41e-05 0.004597
72 MEMBRANE BUDDING 5 114 6.919e-05 0.004597
73 REGULATION OF CELL DIVISION 7 272 7.185e-05 0.004597
74 NEGATIVE REGULATION OF MACROAUTOPHAGY 3 22 7.41e-05 0.004597
75 CELLULAR RESPONSE TO DNA DAMAGE STIMULUS 11 720 7.324e-05 0.004597
76 PROTEIN LOCALIZATION TO MEMBRANE 8 376 8.151e-05 0.004991
77 POSITIVE REGULATION OF TRANSFERASE ACTIVITY 10 616 9.765e-05 0.005901
78 PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM 5 123 9.92e-05 0.005918
79 MEMBRANE ORGANIZATION 12 899 0.0001212 0.007138
80 ESTABLISHMENT OF LOCALIZATION IN CELL 17 1676 0.0001243 0.007229
81 REGULATION OF LIGASE ACTIVITY 5 130 0.0001288 0.007397
82 RRNA MODIFICATION 3 27 0.0001389 0.007879
83 REGULATION OF NEURON PROJECTION DEVELOPMENT 8 408 0.0001432 0.00803
84 NCRNA METABOLIC PROCESS 9 533 0.0001668 0.00924
85 REGULATION OF DNA REPAIR 4 75 0.0001812 0.009811
86 CHROMATIN MODIFICATION 9 539 0.0001813 0.009811
NumGOOverlapSizeP ValueAdj. P Value
1 POLY A RNA BINDING 20 1170 6.889e-09 4.661e-06
2 RNA BINDING 23 1598 1.003e-08 4.661e-06
3 IDENTICAL PROTEIN BINDING 16 1209 8.321e-06 0.002577
NumGOOverlapSizeP ValueAdj. P Value
1 ESCRT III COMPLEX 5 11 2.94e-10 1.717e-07
2 ESCRT COMPLEX 5 26 4.006e-08 1.17e-05
3 RIBONUCLEOPROTEIN COMPLEX 14 721 4.036e-07 7.857e-05
4 NUCLEAR UBIQUITIN LIGASE COMPLEX 4 42 1.832e-05 0.002675
5 NUCLEAR CHROMOSOME 10 523 2.477e-05 0.002893
6 CAJAL BODY 4 52 4.308e-05 0.004193
7 SMALL NUCLEOLAR RIBONUCLEOPROTEIN COMPLEX 3 20 5.515e-05 0.004601
8 ANAPHASE PROMOTING COMPLEX 3 22 7.41e-05 0.005409
9 CHROMOSOME 12 880 9.91e-05 0.00643

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 hsa03015_mRNA_surveillance_pathway 4 83 0.0002679 0.02553
2 hsa04390_Hippo_signaling_pathway 5 154 0.0002836 0.02553
3 hsa04114_Oocyte_meiosis 4 114 0.0008912 0.04109
4 hsa04144_Endocytosis 5 203 0.0009952 0.04109
5 hsa03040_Spliceosome 4 128 0.00137 0.04109
6 hsa04110_Cell_cycle 4 128 0.00137 0.04109
7 hsa04120_Ubiquitin_mediated_proteolysis 4 139 0.001854 0.04767
8 hsa03008_Ribosome_biogenesis_in_eukaryotes 3 81 0.003504 0.07884
9 hsa03010_Ribosome 3 92 0.005008 0.1002
10 hsa04916_Melanogenesis 3 101 0.006488 0.1168
11 hsa04330_Notch_signaling_pathway 2 47 0.01345 0.2201
12 hsa04920_Adipocytokine_signaling_pathway 2 68 0.02695 0.3412
13 hsa04115_p53_signaling_pathway 2 69 0.02769 0.3412
14 hsa04720_Long.term_potentiation 2 70 0.02844 0.3412
15 hsa04730_Long.term_depression 2 70 0.02844 0.3412
16 hsa04662_B_cell_receptor_signaling_pathway 2 75 0.03229 0.3503
17 hsa04370_VEGF_signaling_pathway 2 76 0.03308 0.3503
18 hsa04664_Fc_epsilon_RI_signaling_pathway 2 79 0.03551 0.3551
19 hsa04012_ErbB_signaling_pathway 2 87 0.0423 0.3641
20 hsa04914_Progesterone.mediated_oocyte_maturation 2 87 0.0423 0.3641
21 hsa04151_PI3K_AKT_signaling_pathway 4 351 0.0429 0.3641
22 hsa04540_Gap_junction 2 90 0.04496 0.3641
23 hsa04810_Regulation_of_actin_cytoskeleton 3 214 0.04653 0.3641
24 hsa00240_Pyrimidine_metabolism 2 99 0.05331 0.3977
25 hsa04912_GnRH_signaling_pathway 2 101 0.05523 0.3977
26 hsa04660_T_cell_receptor_signaling_pathway 2 108 0.06216 0.4303
27 hsa04010_MAPK_signaling_pathway 3 268 0.07963 0.5141
28 hsa04722_Neurotrophin_signaling_pathway 2 127 0.0823 0.5141
29 hsa04530_Tight_junction 2 133 0.08903 0.533
30 hsa04650_Natural_killer_cell_mediated_cytotoxicity 2 136 0.09245 0.533
31 hsa04910_Insulin_signaling_pathway 2 138 0.09475 0.533
32 hsa04310_Wnt_signaling_pathway 2 151 0.1101 0.583
33 hsa00230_Purine_metabolism 2 162 0.1236 0.618
34 hsa04510_Focal_adhesion 2 200 0.1727 0.7972
35 hsa04014_Ras_signaling_pathway 2 236 0.2217 0.9501

Quest ID: 7fb3c4862c7d8317c599e18c0c8e4992