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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-151a-3p UCHL1 1.24 0 -1.26 0.0393 MirTarget -0.82 0 NA
2 hsa-miR-429 UCHL1 4.49 0 -1.26 0.0393 miRNATAP -0.46 0 NA
3 hsa-miR-877-5p UCHL1 2.95 0 -1.26 0.0393 miRNAWalker2 validate -0.17 0.03813 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL 17 873 1.298e-09 6.038e-06
2 PROTEIN MODIFICATION BY SMALL PROTEIN REMOVAL 8 133 1.001e-08 2.33e-05
3 PROTEIN CATABOLIC PROCESS 13 579 2.978e-08 4.619e-05
4 MACROMOLECULE CATABOLIC PROCESS 15 926 1.634e-07 0.00019
5 RESPONSE TO INORGANIC SUBSTANCE 11 479 3.139e-07 0.0002709
6 CATABOLIC PROCESS 20 1773 3.493e-07 0.0002709
7 CELLULAR CATABOLIC PROCESS 17 1322 5.588e-07 0.0003714
8 HISTONE H3 DEACETYLATION 4 22 6.679e-07 0.0003884
9 PROTEOLYSIS 16 1208 8.823e-07 0.0004561
10 POSITIVE REGULATION OF TRANSPORT 14 936 1.179e-06 0.0005484
11 STRIATED MUSCLE CELL DIFFERENTIATION 7 173 1.316e-06 0.0005567
12 SINGLE ORGANISM BEHAVIOR 9 384 3.502e-06 0.001358
13 NEUROGENESIS 16 1402 6.112e-06 0.002188
14 CELL DEVELOPMENT 16 1426 7.583e-06 0.00252
15 REGULATION OF TRANSPORT 18 1804 9.105e-06 0.002824
16 MUSCLE CELL DIFFERENTIATION 7 237 1.05e-05 0.003054
17 CELL DEATH 13 1001 1.392e-05 0.003599
18 COVALENT CHROMATIN MODIFICATION 8 345 1.38e-05 0.003599
19 NEGATIVE REGULATION OF NITROGEN COMPOUND METABOLIC PROCESS 16 1517 1.65e-05 0.00404
20 POSITIVE REGULATION OF CELLULAR PROTEIN LOCALIZATION 8 360 1.875e-05 0.004361
21 NEGATIVE REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 11 740 2.052e-05 0.004546
22 RESPONSE TO HYDROGEN PEROXIDE 5 109 2.588e-05 0.005474
23 NEURON DEVELOPMENT 10 687 6.073e-05 0.00713
24 NEGATIVE REGULATION OF GENE EXPRESSION 15 1493 5.646e-05 0.00713
25 MACROMOLECULE DEACYLATION 4 67 6.282e-05 0.00713
26 NEURON PROJECTION DEVELOPMENT 9 545 5.627e-05 0.00713
27 POSITIVE REGULATION OF PROTEIN LOCALIZATION TO NUCLEUS 5 129 5.805e-05 0.00713
28 REGULATION OF CELLULAR LOCALIZATION 14 1277 4.092e-05 0.00713
29 POSITIVE REGULATION OF NUCLEOCYTOPLASMIC TRANSPORT 5 121 4.276e-05 0.00713
30 REGULATION OF PROTEIN LOCALIZATION 12 950 4.115e-05 0.00713
31 INTERSPECIES INTERACTION BETWEEN ORGANISMS 10 662 4.45e-05 0.00713
32 REGULATION OF CYSTEINE TYPE ENDOPEPTIDASE ACTIVITY 6 213 6.094e-05 0.00713
33 REGULATION OF CELL DEATH 15 1472 4.799e-05 0.00713
34 NEGATIVE REGULATION OF CYTOKINE PRODUCTION 6 211 5.784e-05 0.00713
35 REGULATION OF CELLULAR PROTEIN LOCALIZATION 9 552 6.208e-05 0.00713
36 NEGATIVE REGULATION OF MULTICELLULAR ORGANISMAL PROCESS 12 983 5.727e-05 0.00713
37 MUSCLE CELL DEVELOPMENT 5 128 5.594e-05 0.00713
38 SYMBIOSIS ENCOMPASSING MUTUALISM THROUGH PARASITISM 10 662 4.45e-05 0.00713
39 REGULATION OF CELL PROLIFERATION 15 1496 5.777e-05 0.00713
40 BEHAVIOR 9 516 3.685e-05 0.00713
41 POSITIVE REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION 9 514 3.575e-05 0.00713
42 DOPAMINE METABOLIC PROCESS 3 25 6.835e-05 0.007228
43 MUSCLE STRUCTURE DEVELOPMENT 8 432 6.82e-05 0.007228
44 NEUROTRANSMITTER METABOLIC PROCESS 3 25 6.835e-05 0.007228
45 NEGATIVE REGULATION OF CELL ADHESION 6 223 7.854e-05 0.008121
46 RESPONSE TO METAL ION 7 333 9.168e-05 0.009189
47 NEURON DIFFERENTIATION 11 874 9.282e-05 0.009189
48 CELLULAR RESPONSE TO STRESS 15 1565 9.637e-05 0.009342
NumGOOverlapSizeP ValueAdj. P Value
1 UBIQUITIN LIKE PROTEIN SPECIFIC PROTEASE ACTIVITY 8 117 3.627e-09 3.37e-06
2 CYSTEINE TYPE PEPTIDASE ACTIVITY 8 184 1.257e-07 3.891e-05
3 THIOL DEPENDENT UBIQUITIN SPECIFIC PROTEASE ACTIVITY 6 73 1.216e-07 3.891e-05
4 NAD DEPENDENT PROTEIN DEACETYLASE ACTIVITY 4 17 2.199e-07 5.108e-05
5 HYDROLASE ACTIVITY ACTING ON CARBON NITROGEN BUT NOT PEPTIDE BONDS IN LINEAR AMIDES 5 84 7.272e-06 0.0009651
6 HISTONE DEACETYLASE ACTIVITY H3 K14 SPECIFIC 3 12 6.735e-06 0.0009651
7 LIGASE ACTIVITY 9 406 5.5e-06 0.0009651
8 PROTEIN DEACETYLASE ACTIVITY 4 43 1.071e-05 0.001244
9 DEACETYLASE ACTIVITY 4 55 2.877e-05 0.00297
10 PEPTIDASE ACTIVITY 10 663 4.507e-05 0.004187
11 HYDROLASE ACTIVITY ACTING ON CARBON NITROGEN BUT NOT PEPTIDE BONDS 5 143 9.463e-05 0.007992
12 MACROMOLECULAR COMPLEX BINDING 14 1399 0.0001096 0.008486
NumGOOverlapSizeP ValueAdj. P Value

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 Tight_junction_hsa04530 5 170 0.0002127 0.01106
2 Adherens_junction_hsa04520 3 72 0.001592 0.0414
3 Focal_adhesion_hsa04510 4 199 0.003793 0.06575
4 Endocytosis_hsa04144 4 244 0.00775 0.09763
5 Notch_signaling_pathway_hsa04330 2 48 0.01034 0.09763
6 Cell_adhesion_molecules_.CAMs._hsa04514 3 145 0.01126 0.09763
7 VEGF_signaling_pathway_hsa04370 2 59 0.01534 0.114
8 Mitophagy_animal_hsa04137 2 65 0.01842 0.1189
9 Calcium_signaling_pathway_hsa04020 3 182 0.02059 0.1189
10 PI3K_Akt_signaling_pathway_hsa04151 4 352 0.02623 0.1315
11 Rap1_signaling_pathway_hsa04015 3 206 0.02835 0.1315
12 ErbB_signaling_pathway_hsa04012 2 85 0.03036 0.1315
13 HIF_1_signaling_pathway_hsa04066 2 100 0.04083 0.1633
14 Cell_cycle_hsa04110 2 124 0.05993 0.2209
15 FoxO_signaling_pathway_hsa04068 2 132 0.06687 0.2209
16 MAPK_signaling_pathway_hsa04010 3 295 0.06863 0.2209
17 Apoptosis_hsa04210 2 138 0.07223 0.2209
18 Cellular_senescence_hsa04218 2 160 0.09302 0.2687
19 Regulation_of_actin_cytoskeleton_hsa04810 2 208 0.1431 0.3545
20 Ras_signaling_pathway_hsa04014 2 232 0.17 0.4018

Quest ID: ab9d64704c58857e77017641934228f1