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.
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-615-3p | UBE2C | -0.78 | 0 | 3.36 | 0 | miRNAWalker2 validate | -0.28 | 0.00828 | NA |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|
1 | PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL | 20 | 873 | 5.744e-16 | 2.673e-12 |
2 | PROTEIN POLYUBIQUITINATION | 11 | 243 | 4.791e-12 | 7.431e-09 |
3 | PROTEIN UBIQUITINATION | 15 | 629 | 3.555e-12 | 7.431e-09 |
4 | PROTEIN K48 LINKED UBIQUITINATION | 7 | 47 | 1.052e-11 | 1.224e-08 |
5 | PROTEIN CATABOLIC PROCESS | 14 | 579 | 1.816e-11 | 1.69e-08 |
6 | PROTEASOMAL PROTEIN CATABOLIC PROCESS | 10 | 271 | 3.714e-10 | 2.881e-07 |
7 | PROTEIN MONOUBIQUITINATION | 6 | 51 | 1.532e-09 | 1.018e-06 |
8 | REGULATION OF MITOTIC CELL CYCLE | 11 | 468 | 5.075e-09 | 2.952e-06 |
9 | MACROMOLECULE CATABOLIC PROCESS | 14 | 926 | 8.224e-09 | 4.252e-06 |
10 | REGULATION OF PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL | 9 | 280 | 1.036e-08 | 4.821e-06 |
11 | POSITIVE REGULATION OF PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL | 8 | 196 | 1.165e-08 | 4.929e-06 |
12 | PROTEOLYSIS | 15 | 1208 | 2.948e-08 | 1.143e-05 |
13 | POSITIVE REGULATION OF PROTEIN METABOLIC PROCESS | 16 | 1492 | 6.881e-08 | 2.319e-05 |
14 | REGULATION OF PROTEIN MODIFICATION PROCESS | 17 | 1710 | 6.977e-08 | 2.319e-05 |
15 | CELLULAR CATABOLIC PROCESS | 15 | 1322 | 9.7e-08 | 2.728e-05 |
16 | REGULATION OF TRANSFERASE ACTIVITY | 13 | 946 | 9.736e-08 | 2.728e-05 |
17 | REGULATION OF CELL CYCLE | 13 | 949 | 1.01e-07 | 2.728e-05 |
18 | POSITIVE REGULATION OF PROTEIN MODIFICATION PROCESS | 14 | 1135 | 1.055e-07 | 2.728e-05 |
19 | REGULATION OF LIGASE ACTIVITY | 6 | 130 | 4.443e-07 | 0.0001088 |
20 | PROTEIN UBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS | 6 | 134 | 5.313e-07 | 0.0001177 |
21 | REGULATION OF CELL CYCLE PHASE TRANSITION | 8 | 321 | 5.19e-07 | 0.0001177 |
22 | MITOTIC CELL CYCLE | 11 | 766 | 7.467e-07 | 0.0001511 |
23 | CATABOLIC PROCESS | 16 | 1773 | 7.303e-07 | 0.0001511 |
24 | ORGANELLE FISSION | 9 | 496 | 1.322e-06 | 0.0002563 |
25 | PROSTATE GLAND GROWTH | 3 | 11 | 1.734e-06 | 0.0003228 |
26 | PROSTATE GLAND DEVELOPMENT | 4 | 41 | 2.131e-06 | 0.0003813 |
27 | REGULATION OF PROTEIN CATABOLIC PROCESS | 8 | 393 | 2.363e-06 | 0.0004055 |
28 | REGULATION OF CELLULAR PROTEIN CATABOLIC PROCESS | 7 | 274 | 2.44e-06 | 0.0004055 |
29 | CELL CYCLE PROCESS | 12 | 1081 | 3.199e-06 | 0.0005132 |
30 | REGULATION OF PROTEIN UBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS | 5 | 103 | 3.408e-06 | 0.0005214 |
31 | REGULATION OF CELL CYCLE PROCESS | 9 | 558 | 3.474e-06 | 0.0005214 |
32 | REGULATION OF CATABOLIC PROCESS | 10 | 731 | 4.002e-06 | 0.0005779 |
33 | CELL CYCLE | 13 | 1316 | 4.099e-06 | 0.0005779 |
34 | PROTEIN AUTOUBIQUITINATION | 4 | 49 | 4.4e-06 | 0.0006021 |
35 | POSITIVE REGULATION OF LIGASE ACTIVITY | 5 | 110 | 4.709e-06 | 0.000626 |
36 | POSITIVE REGULATION OF TRANSFERASE ACTIVITY | 9 | 616 | 7.736e-06 | 0.0009998 |
37 | POSITIVE REGULATION OF CELL PROLIFERATION | 10 | 814 | 1.031e-05 | 0.001297 |
38 | RESPONSE TO ENDOGENOUS STIMULUS | 13 | 1450 | 1.178e-05 | 0.001443 |
39 | RESPONSE TO STEROID HORMONE | 8 | 497 | 1.32e-05 | 0.001575 |
40 | MITOTIC NUCLEAR DIVISION | 7 | 361 | 1.481e-05 | 0.001723 |
41 | ORGAN GROWTH | 4 | 68 | 1.639e-05 | 0.00186 |
42 | INTRACELLULAR STEROID HORMONE RECEPTOR SIGNALING PATHWAY | 4 | 71 | 1.946e-05 | 0.002156 |
43 | POSITIVE REGULATION OF MOLECULAR FUNCTION | 14 | 1791 | 2.356e-05 | 0.002549 |
44 | REGULATION OF PROTEOLYSIS | 9 | 711 | 2.423e-05 | 0.002563 |
45 | POSITIVE REGULATION OF PROTEIN CATABOLIC PROCESS | 6 | 263 | 2.588e-05 | 0.002614 |
46 | POSITIVE REGULATION OF CATABOLIC PROCESS | 7 | 395 | 2.641e-05 | 0.002614 |
47 | GLAND DEVELOPMENT | 7 | 395 | 2.641e-05 | 0.002614 |
48 | PROTEIN K11 LINKED UBIQUITINATION | 3 | 27 | 2.998e-05 | 0.002906 |
49 | REPRODUCTIVE SYSTEM DEVELOPMENT | 7 | 408 | 3.247e-05 | 0.003083 |
50 | REGULATION OF PHOSPHORUS METABOLIC PROCESS | 13 | 1618 | 3.781e-05 | 0.003518 |
51 | REGULATION OF KINASE ACTIVITY | 9 | 776 | 4.803e-05 | 0.004382 |
52 | CELL DIVISION | 7 | 460 | 6.931e-05 | 0.005864 |
53 | POSITIVE REGULATION OF CELLULAR PROTEIN CATABOLIC PROCESS | 5 | 192 | 6.924e-05 | 0.005864 |
54 | NEGATIVE REGULATION OF CELL CYCLE G1 S PHASE TRANSITION | 4 | 98 | 6.922e-05 | 0.005864 |
55 | REGULATION OF CYCLIN DEPENDENT PROTEIN KINASE ACTIVITY | 4 | 97 | 6.651e-05 | 0.005864 |
56 | NEGATIVE REGULATION OF MITOTIC CELL CYCLE | 5 | 199 | 8.2e-05 | 0.006814 |
57 | POSITIVE REGULATION OF CATALYTIC ACTIVITY | 12 | 1518 | 9.522e-05 | 0.007773 |
58 | ANDROGEN RECEPTOR SIGNALING PATHWAY | 3 | 41 | 0.0001069 | 0.008574 |
59 | NEGATIVE REGULATION OF MOLECULAR FUNCTION | 10 | 1079 | 0.0001134 | 0.008941 |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|
1 | UBIQUITIN LIKE PROTEIN TRANSFERASE ACTIVITY | 14 | 420 | 2.414e-13 | 2.243e-10 |
2 | UBIQUITIN LIKE PROTEIN LIGASE ACTIVITY | 9 | 199 | 5.185e-10 | 2.409e-07 |
3 | LIGASE ACTIVITY | 10 | 406 | 1.801e-08 | 5.577e-06 |
4 | UBIQUITIN LIKE PROTEIN CONJUGATING ENZYME ACTIVITY | 4 | 29 | 5.096e-07 | 0.0001029 |
5 | ENZYME BINDING | 16 | 1737 | 5.538e-07 | 0.0001029 |
6 | UBIQUITIN LIKE PROTEIN LIGASE BINDING | 7 | 264 | 1.907e-06 | 0.0002952 |
7 | BETA CATENIN BINDING | 4 | 84 | 3.783e-05 | 0.005021 |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|
1 | UBIQUITIN LIGASE COMPLEX | 10 | 262 | 2.673e-10 | 1.561e-07 |
2 | CATALYTIC COMPLEX | 15 | 1038 | 3.838e-09 | 1.121e-06 |
3 | TRANSFERASE COMPLEX | 12 | 703 | 3.212e-08 | 6.252e-06 |
4 | NUCLEAR UBIQUITIN LIGASE COMPLEX | 4 | 42 | 2.351e-06 | 0.0003433 |
Num | Pathway | Pathview | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|---|
1 | hsa04120_Ubiquitin_mediated_proteolysis | 11 | 139 | 1.014e-14 | 1.826e-12 | |
2 | hsa04141_Protein_processing_in_endoplasmic_reticulum | 5 | 168 | 3.668e-05 | 0.003301 | |
3 | hsa04151_PI3K_AKT_signaling_pathway | 6 | 351 | 0.000128 | 0.00768 | |
4 | hsa04115_p53_signaling_pathway | 3 | 69 | 0.0005027 | 0.02262 | |
5 | hsa04510_Focal_adhesion | 4 | 200 | 0.001049 | 0.03777 | |
6 | hsa04110_Cell_cycle | 3 | 128 | 0.002986 | 0.08959 | |
7 | hsa04350_TGF.beta_signaling_pathway | 2 | 85 | 0.0157 | 0.4037 | |
8 | hsa04114_Oocyte_meiosis | 2 | 114 | 0.02719 | 0.6117 | |
9 | hsa04310_Wnt_signaling_pathway | 2 | 151 | 0.04538 | 0.8266 | |
10 | hsa04630_Jak.STAT_signaling_pathway | 2 | 155 | 0.04755 | 0.8266 | |
11 | hsa04020_Calcium_signaling_pathway | 2 | 177 | 0.06018 | 0.9027 | |
12 | hsa04144_Endocytosis | 2 | 203 | 0.0764 | 1 | |
13 | hsa04014_Ras_signaling_pathway | 2 | 236 | 0.0987 | 1 |