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
| 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-204-5p | ADAM12 | -1.02 | 0.00767 | 2.41 | 0 | mirMAP | -0.13 | 0.01292 | NA | |
| 2 | hsa-miR-204-5p | B4GALT1 | -1.02 | 0.00767 | 0.36 | 0.02384 | miRNATAP | -0.11 | 0 | NA | |
| 3 | hsa-miR-204-5p | BEND6 | -1.02 | 0.00767 | 1.02 | 0.00304 | mirMAP | -0.11 | 0.00913 | NA | |
| 4 | hsa-miR-204-5p | CELSR3 | -1.02 | 0.00767 | 3.19 | 0 | MirTarget; miRNATAP | -0.13 | 0.00501 | NA | |
| 5 | hsa-miR-204-5p | CENPL | -1.02 | 0.00767 | 1.21 | 0 | MirTarget | -0.14 | 0 | NA | |
| 6 | hsa-miR-204-5p | CHML | -1.02 | 0.00767 | 1.06 | 4.0E-5 | mirMAP | -0.1 | 0.00104 | NA | |
| 7 | hsa-miR-204-5p | CNNM4 | -1.02 | 0.00767 | 0.16 | 0.31485 | miRNATAP | -0.12 | 0 | NA | |
| 8 | hsa-miR-204-5p | CPD | -1.02 | 0.00767 | 0.91 | 9.0E-5 | miRNATAP | -0.13 | 0 | NA | |
| 9 | hsa-miR-204-5p | CPNE8 | -1.02 | 0.00767 | 0.03 | 0.85807 | MirTarget; miRNATAP | -0.14 | 0 | NA | |
| 10 | hsa-miR-204-5p | ELOVL6 | -1.02 | 0.00767 | 0.82 | 0.02787 | miRNAWalker2 validate; miRTarBase; MirTarget; miRNATAP | -0.13 | 0.00525 | NA | |
| 11 | hsa-miR-204-5p | ENO1 | -1.02 | 0.00767 | 1.02 | 0 | miRNAWalker2 validate | -0.11 | 0 | NA | |
| 12 | hsa-miR-204-5p | EPHB2 | -1.02 | 0.00767 | 1.8 | 0 | MirTarget | -0.12 | 0.00266 | NA | |
| 13 | hsa-miR-204-5p | ESCO2 | -1.02 | 0.00767 | 2.42 | 0 | MirTarget | -0.17 | 1.0E-5 | NA | |
| 14 | hsa-miR-204-5p | FAM114A1 | -1.02 | 0.00767 | 0.58 | 0.00084 | MirTarget | -0.1 | 0 | NA | |
| 15 | hsa-miR-204-5p | FBXO32 | -1.02 | 0.00767 | 1.92 | 0 | mirMAP | -0.15 | 0 | NA | |
| 16 | hsa-miR-204-5p | FERMT1 | -1.02 | 0.00767 | 2.71 | 0 | MirTarget | -0.11 | 0.00829 | NA | |
| 17 | hsa-miR-204-5p | HMGA2 | -1.02 | 0.00767 | 3.12 | 0.00011 | miRNATAP | -0.28 | 0.005 | 27095441; 26406941 | We identified high mobility group protein A2 HMGA2 as a novel direct target of miR-204 and showed that miR-204 expression was decreased while HMGA2 expression was increased in CRC cell lines; Additionally both MiR-204 overexpression and HMGA2 inhibition attenuated cell proliferation whereas forced expression of HMGA2 partly restored the inhibitory effect of miR-204 on HCT116 and SW480 cells; Taken together our present study elucidated that miR-204 upregulated 5-Fu chemosensitivity via the downregulation of HMGA2 in colorectal cancer and provided significant insight into the mechanism of 5-Fu resistance in colorectal cancer patients;MiR 204 regulates HMGA2 expression and inhibits cell proliferation in human thyroid cancer; Analysis using publicly available algorithms has found that high mobility group AT-hook 2 HMGA2 a key transcriptional regulatory factor is a potential target of microRNA-204 miR-204; Some studies have shown that both miR-204 and HMGA2 are associated with cancer development; We examined the possible relationship between miR-204 and HMGA2 in the development of thyroid cancer; MiR-204 was downregulated in the thyroid cancer specimens and cell lines and targeted the 3^\prime untranslated region of HMGA2 directly |
| 18 | hsa-miR-204-5p | HOXA10 | -1.02 | 0.00767 | 2.3 | 0.00036 | miRNAWalker2 validate; miRTarBase | -0.24 | 0.00253 | 18308931 | Indeed we confirmed that miR-204 targets HOXA10 and MEIS1 suggesting that the HOX up-regulation observed in NPMc+ AML may be due in part by loss of HOX regulators-miRNAs |
| 19 | hsa-miR-204-5p | IER5L | -1.02 | 0.00767 | 1.66 | 0 | miRNATAP | -0.12 | 0.00071 | NA | |
| 20 | hsa-miR-204-5p | IL11 | -1.02 | 0.00767 | 1.89 | 0 | miRNAWalker2 validate; miRTarBase; MirTarget | -0.13 | 0.00802 | NA | |
| 21 | hsa-miR-204-5p | IL1RAP | -1.02 | 0.00767 | 0 | 0.99919 | miRNAWalker2 validate | -0.11 | 0.00018 | NA | |
| 22 | hsa-miR-204-5p | ITGB3 | -1.02 | 0.00767 | 0.05 | 0.90111 | miRNAWalker2 validate | -0.11 | 0.01335 | NA | |
| 23 | hsa-miR-204-5p | LGR4 | -1.02 | 0.00767 | 2.49 | 0 | MirTarget | -0.17 | 0 | NA | |
| 24 | hsa-miR-204-5p | PERP | -1.02 | 0.00767 | 0.78 | 0.00023 | MirTarget | -0.13 | 0 | NA | |
| 25 | hsa-miR-204-5p | PLAT | -1.02 | 0.00767 | 0.19 | 0.62686 | miRNAWalker2 validate | -0.13 | 0.00791 | NA | |
| 26 | hsa-miR-204-5p | PLAUR | -1.02 | 0.00767 | 0.08 | 0.75711 | miRNAWalker2 validate | -0.14 | 0 | NA | |
| 27 | hsa-miR-204-5p | SASS6 | -1.02 | 0.00767 | 1.2 | 0 | MirTarget | -0.12 | 0 | NA | |
| 28 | hsa-miR-204-5p | SATB2 | -1.02 | 0.00767 | 0.86 | 0.00169 | miRNATAP | -0.15 | 0 | NA | |
| 29 | hsa-miR-204-5p | SLC5A3 | -1.02 | 0.00767 | 0.91 | 2.0E-5 | mirMAP | -0.11 | 4.0E-5 | NA | |
| 30 | hsa-miR-204-5p | TFAP2A | -1.02 | 0.00767 | 3.63 | 0 | miRNATAP | -0.24 | 1.0E-5 | NA | |
| 31 | hsa-miR-204-5p | TTYH1 | -1.02 | 0.00767 | 2.03 | 0 | miRNATAP | -0.16 | 0.00078 | NA | |
| 32 | hsa-miR-204-5p | UGDH | -1.02 | 0.00767 | 1.39 | 0 | MirTarget | -0.15 | 2.0E-5 | NA | |
| 33 | hsa-miR-204-5p | WDR76 | -1.02 | 0.00767 | 0.85 | 4.0E-5 | MirTarget | -0.13 | 0 | NA |
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|
Over-represented Pathway
| Num | Pathway | Pathview | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|---|
| 1 | Cytokine_cytokine_receptor_interaction_hsa04060 | 2 | 270 | 0.07293 | 1 |
