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-9-5p | ACADSB | 1.26 | 9.0E-5 | -2.11 | 0 | miRNAWalker2 validate | -0.16 | 0 | NA | |
2 | hsa-miR-9-5p | ANO1 | 1.26 | 9.0E-5 | -2.23 | 0 | MirTarget; miRNATAP | -0.19 | 0.00016 | NA | |
3 | hsa-miR-9-5p | AR | 1.26 | 9.0E-5 | -2.66 | 0 | miRNATAP | -0.21 | 0.00072 | NA | |
4 | hsa-miR-9-5p | BMPER | 1.26 | 9.0E-5 | -6.23 | 0 | miRNATAP | -0.19 | 0.00341 | NA | |
5 | hsa-miR-9-5p | CBLN4 | 1.26 | 9.0E-5 | -1.67 | 0.00015 | miRNATAP | -0.22 | 0.00113 | NA | |
6 | hsa-miR-9-5p | CCND1 | 1.26 | 9.0E-5 | -0.9 | 1.0E-5 | miRNAWalker2 validate | -0.14 | 1.0E-5 | NA | |
7 | hsa-miR-9-5p | CDC14B | 1.26 | 9.0E-5 | -1.19 | 0 | MirTarget | -0.11 | 5.0E-5 | NA | |
8 | hsa-miR-9-5p | CHST9 | 1.26 | 9.0E-5 | -2.33 | 0 | miRNATAP | -0.15 | 0.03281 | NA | |
9 | hsa-miR-9-5p | CLDN14 | 1.26 | 9.0E-5 | -0.82 | 0.00105 | MirTarget | -0.16 | 3.0E-5 | NA | |
10 | hsa-miR-9-5p | CLYBL | 1.26 | 9.0E-5 | -1.25 | 0 | mirMAP | -0.13 | 0 | NA | |
11 | hsa-miR-9-5p | COL18A1 | 1.26 | 9.0E-5 | -0.88 | 0 | miRNATAP | -0.12 | 0 | NA | |
12 | hsa-miR-9-5p | CPEB3 | 1.26 | 9.0E-5 | -2.74 | 0 | MirTarget; miRNATAP | -0.19 | 0 | NA | |
13 | hsa-miR-9-5p | CYP39A1 | 1.26 | 9.0E-5 | -4.33 | 0 | miRNAWalker2 validate | -0.3 | 2.0E-5 | NA | |
14 | hsa-miR-9-5p | ESR1 | 1.26 | 9.0E-5 | -4.12 | 0 | mirMAP; miRNATAP | -0.3 | 0 | 22723919 | Higher expression of miR-9 was significantly associated with breast cancer LR in all cases as well as the subset of estrogen receptor ER positive cases p = 0.02 |
15 | hsa-miR-9-5p | F2 | 1.26 | 9.0E-5 | -1.49 | 0 | miRNAWalker2 validate | -0.12 | 0.00663 | NA | |
16 | hsa-miR-9-5p | FLRT3 | 1.26 | 9.0E-5 | -1.64 | 0 | MirTarget; miRNATAP | -0.16 | 8.0E-5 | NA | |
17 | hsa-miR-9-5p | FOXO1 | 1.26 | 9.0E-5 | -1.85 | 0 | miRNAWalker2 validate; miRTarBase; miRNATAP | -0.16 | 0 | 24870723; 25017439 | Phosphorylation of Akt and forkhead box protein O1 FOXO1 was measured in cells with miR-9 overexpression or curcumin treatment; Western blot analysis showed that both miR-9 overexpression and curcumin similarly caused a significant p<0.05 decline in the phosphorylation of Akt and FOXO1 compared to untreated cells;In this study we explored whether FOXO1 3'UTR can function as a ceRNA in repressing epithelial-to-mesenchymal transition EMT and metastasis of breast cancer cells via regulating miR-9 activity; Follow-up analyses showed that there existed a competition of miR-9 between FOXO1 and E-cadherin-3'UTR |
18 | hsa-miR-9-5p | FOXP2 | 1.26 | 9.0E-5 | -3.25 | 0 | MirTarget | -0.19 | 0.00331 | NA | |
19 | hsa-miR-9-5p | GFRA1 | 1.26 | 9.0E-5 | -2.55 | 0 | mirMAP | -0.28 | 7.0E-5 | NA | |
20 | hsa-miR-9-5p | GNAO1 | 1.26 | 9.0E-5 | -3.67 | 0 | mirMAP | -0.14 | 0.02412 | NA | |
21 | hsa-miR-9-5p | GOT1 | 1.26 | 9.0E-5 | -1.38 | 0 | MirTarget; miRNATAP | -0.13 | 1.0E-5 | NA | |
22 | hsa-miR-9-5p | GPAM | 1.26 | 9.0E-5 | -0.47 | 0.0638 | miRNATAP | -0.21 | 0 | NA | |
23 | hsa-miR-9-5p | GREB1 | 1.26 | 9.0E-5 | 0.43 | 0.16751 | MirTarget; miRNATAP | -0.1 | 0.03338 | NA | |
24 | hsa-miR-9-5p | HS3ST3B1 | 1.26 | 9.0E-5 | -2.61 | 0 | mirMAP | -0.2 | 3.0E-5 | NA | |
25 | hsa-miR-9-5p | IGF2 | 1.26 | 9.0E-5 | -3.69 | 0 | mirMAP | -0.45 | 0 | NA | |
26 | hsa-miR-9-5p | INSIG1 | 1.26 | 9.0E-5 | -0.98 | 0.00012 | MirTarget; miRNATAP | -0.11 | 0.00362 | NA | |
27 | hsa-miR-9-5p | IYD | 1.26 | 9.0E-5 | -2.66 | 0 | mirMAP | -0.18 | 0.00095 | NA | |
28 | hsa-miR-9-5p | KLF12 | 1.26 | 9.0E-5 | -0.86 | 0 | mirMAP | -0.11 | 0 | NA | |
29 | hsa-miR-9-5p | KLHDC7A | 1.26 | 9.0E-5 | -0.99 | 0.0002 | MirTarget | -0.12 | 0.00215 | NA | |
30 | hsa-miR-9-5p | MYLK | 1.26 | 9.0E-5 | -1.14 | 0 | miRNAWalker2 validate | -0.1 | 0.00011 | NA | |
31 | hsa-miR-9-5p | NFIA | 1.26 | 9.0E-5 | -0.92 | 0 | mirMAP; miRNATAP | -0.11 | 0 | NA | |
32 | hsa-miR-9-5p | OGDHL | 1.26 | 9.0E-5 | -2.53 | 0 | MirTarget | -0.15 | 0.00839 | NA | |
33 | hsa-miR-9-5p | PALM2 | 1.26 | 9.0E-5 | -2.08 | 0 | mirMAP | -0.11 | 0.00199 | NA | |
34 | hsa-miR-9-5p | PALMD | 1.26 | 9.0E-5 | -0.6 | 0.00198 | MirTarget; miRNATAP | -0.15 | 0 | NA | |
35 | hsa-miR-9-5p | PCSK6 | 1.26 | 9.0E-5 | -1.19 | 0 | MirTarget; miRNATAP | -0.13 | 3.0E-5 | NA | |
36 | hsa-miR-9-5p | PDE7B | 1.26 | 9.0E-5 | -2.16 | 0 | miRNATAP | -0.14 | 2.0E-5 | NA | |
37 | hsa-miR-9-5p | PDK4 | 1.26 | 9.0E-5 | -2.11 | 0 | MirTarget; miRNATAP | -0.15 | 0.00032 | NA | |
38 | hsa-miR-9-5p | PITPNM3 | 1.26 | 9.0E-5 | -3.87 | 0 | mirMAP; miRNATAP | -0.14 | 0.00296 | NA | |
39 | hsa-miR-9-5p | PTCH1 | 1.26 | 9.0E-5 | -0.78 | 8.0E-5 | miRNATAP | -0.1 | 0.0005 | 25595896 | Computational studies real-time PCR reporter gene studies western blots target protector oligos and ectopic expression identified miR-9 as the target of PTCH1 in resistant GBM cells with concomitant activation of SHH signaling; Taken together miR-9 targets PTCH1 in GBM cells by a SHH-independent method in GBM cells for TMZ resistance |
40 | hsa-miR-9-5p | RASGEF1B | 1.26 | 9.0E-5 | -2.4 | 0 | mirMAP | -0.11 | 0.00252 | NA | |
41 | hsa-miR-9-5p | RNF165 | 1.26 | 9.0E-5 | -3.06 | 0 | mirMAP | -0.15 | 0.00276 | NA | |
42 | hsa-miR-9-5p | RORA | 1.26 | 9.0E-5 | -1.19 | 0 | mirMAP; miRNATAP | -0.12 | 0 | NA | |
43 | hsa-miR-9-5p | RTN4RL1 | 1.26 | 9.0E-5 | 0.06 | 0.81318 | MirTarget | -0.13 | 0.00161 | NA | |
44 | hsa-miR-9-5p | RUNDC3B | 1.26 | 9.0E-5 | -1.77 | 0 | miRNATAP | -0.19 | 0 | NA | |
45 | hsa-miR-9-5p | SH3BGRL2 | 1.26 | 9.0E-5 | -0.97 | 0 | miRNATAP | -0.11 | 0 | NA | |
46 | hsa-miR-9-5p | SH3BP4 | 1.26 | 9.0E-5 | -0.17 | 0.23449 | miRNATAP | -0.11 | 0 | NA | |
47 | hsa-miR-9-5p | SIK1 | 1.26 | 9.0E-5 | -1.56 | 0 | miRNATAP | -0.11 | 0.00066 | NA | |
48 | hsa-miR-9-5p | SLC16A2 | 1.26 | 9.0E-5 | -1.72 | 0 | miRNATAP | -0.16 | 1.0E-5 | NA | |
49 | hsa-miR-9-5p | SLC1A1 | 1.26 | 9.0E-5 | -2.49 | 0 | miRNATAP | -0.12 | 0.04073 | NA | |
50 | hsa-miR-9-5p | SLC1A2 | 1.26 | 9.0E-5 | -2.05 | 1.0E-5 | mirMAP | -0.19 | 0.00488 | NA | |
51 | hsa-miR-9-5p | SLC20A2 | 1.26 | 9.0E-5 | -0.68 | 0 | miRNATAP | -0.12 | 0 | NA | |
52 | hsa-miR-9-5p | SLC22A3 | 1.26 | 9.0E-5 | -1.99 | 0 | miRNAWalker2 validate | -0.17 | 9.0E-5 | NA | |
53 | hsa-miR-9-5p | SLC25A30 | 1.26 | 9.0E-5 | -0.36 | 0.03319 | miRNAWalker2 validate | -0.11 | 2.0E-5 | NA | |
54 | hsa-miR-9-5p | SMOC1 | 1.26 | 9.0E-5 | -1.11 | 0 | mirMAP | -0.12 | 3.0E-5 | NA | |
55 | hsa-miR-9-5p | SNED1 | 1.26 | 9.0E-5 | -0.7 | 1.0E-5 | mirMAP | -0.13 | 0 | NA | |
56 | hsa-miR-9-5p | STEAP3 | 1.26 | 9.0E-5 | -2.25 | 0 | MirTarget | -0.13 | 0.00033 | NA | |
57 | hsa-miR-9-5p | TSPAN9 | 1.26 | 9.0E-5 | -0.77 | 0 | miRNATAP | -0.11 | 0 | NA |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|
1 | RESPONSE TO ENDOGENOUS STIMULUS | 16 | 1450 | 1.801e-06 | 0.00838 |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|
1 | TRANSCRIPTION COACTIVATOR BINDING | 3 | 11 | 3.563e-06 | 0.00331 |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|
Num | Pathway | Pathview | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|---|
1 | Hedgehog_signaling_pathway_hsa04340 | 2 | 47 | 0.007946 | 0.4132 | |
2 | p53_signaling_pathway_hsa04115 | 2 | 68 | 0.01612 | 0.4191 | |
3 | AMPK_signaling_pathway_hsa04152 | 2 | 121 | 0.04669 | 0.4325 | |
4 | Cell_cycle_hsa04110 | 2 | 124 | 0.04878 | 0.4325 | |
5 | Oocyte_meiosis_hsa04114 | 2 | 124 | 0.04878 | 0.4325 | |
6 | FoxO_signaling_pathway_hsa04068 | 2 | 132 | 0.05452 | 0.4325 | |
7 | Apelin_signaling_pathway_hsa04371 | 2 | 137 | 0.05822 | 0.4325 | |
8 | Cellular_senescence_hsa04218 | 2 | 160 | 0.0763 | 0.4891 | |
9 | Tight_junction_hsa04530 | 2 | 170 | 0.08466 | 0.4891 | |
10 | Focal_adhesion_hsa04510 | 2 | 199 | 0.1103 | 0.5141 | |
11 | Regulation_of_actin_cytoskeleton_hsa04810 | 2 | 208 | 0.1186 | 0.5141 | |
12 | PI3K_Akt_signaling_pathway_hsa04151 | 2 | 352 | 0.2654 | 1 |