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-17-5p | EGFR | 0.7 | 2.0E-5 | -1.02 | 0 | TargetScan | -0.16 | 0.00764 | NA | |
2 | hsa-miR-17-5p | EGLN1 | 0.7 | 2.0E-5 | 0.08 | 0.4055 | TargetScan | -0.1 | 9.0E-5 | NA | |
3 | hsa-miR-17-5p | HIF1A | 0.7 | 2.0E-5 | -0.37 | 0.0111 | TargetScan | -0.21 | 0 | NA | |
4 | hsa-miR-17-5p | JAK1 | 0.7 | 2.0E-5 | -0.49 | 0 | TargetScan | -0.27 | 0 | NA | |
5 | hsa-miR-17-5p | PIK3R1 | 0.7 | 2.0E-5 | -0.89 | 0 | TargetScan | -0.21 | 0 | NA | |
6 | hsa-miR-17-5p | ROCK2 | 0.7 | 2.0E-5 | -0.34 | 0.09781 | TargetScan | -0.23 | 0.00013 | NA | |
7 | hsa-miR-17-5p | TGFBR2 | 0.7 | 2.0E-5 | -0.52 | 3.0E-5 | TargetScan | -0.2 | 0 | 25011053; 27120811 | We demonstrate that miR-17 overexpression interferes with the TGFβ-EMT axis and hinders RCC sphere formation; and validated TGFBR2 as a direct and biologically relevant target during this process;MiR-17-5p was found to bind to the 3'UTR of TGFBR2 mRNA and further validation of this specific binding was performed through a reporter assay; An inverse correlation between miR-17-5p and TGFBR2 protein was observed in gastric cancer tissues; Cell studies revealed that miR-17-5p negatively regulated TGFBR2 expression by directly binding to the 3'UTR of TGFBR2 mRNA thereby promoting cell growth and migration; The results of our study suggest a novel regulatory network in gastric cancer mediated by miR-17-5p and TGFBR2 and may indicate that TGFBR2 could serve as a new therapeutic target in gastric cancer |
8 | hsa-miR-501-3p | TGFBR2 | 1 | 0 | -0.52 | 3.0E-5 | TargetScan | -0.12 | 0.00378 | NA |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|
1 | REGULATION OF VASCULATURE DEVELOPMENT | 5 | 233 | 4.237e-09 | 1.971e-05 |
2 | POSITIVE REGULATION OF LOCOMOTION | 5 | 420 | 8.091e-08 | 0.0001882 |
3 | RESPONSE TO OXYGEN CONTAINING COMPOUND | 6 | 1381 | 7.068e-07 | 0.001096 |
4 | ENZYME LINKED RECEPTOR PROTEIN SIGNALING PATHWAY | 5 | 689 | 9.483e-07 | 0.001103 |
5 | EMBRYONIC PLACENTA DEVELOPMENT | 3 | 83 | 2.383e-06 | 0.001232 |
6 | IN UTERO EMBRYONIC DEVELOPMENT | 4 | 311 | 1.935e-06 | 0.001232 |
7 | REGULATION OF MULTICELLULAR ORGANISMAL DEVELOPMENT | 6 | 1672 | 2.201e-06 | 0.001232 |
8 | REGULATION OF CELLULAR COMPONENT MOVEMENT | 5 | 771 | 1.655e-06 | 0.001232 |
9 | REGULATION OF PHOSPHORUS METABOLIC PROCESS | 6 | 1618 | 1.811e-06 | 0.001232 |
10 | RESPONSE TO HORMONE | 5 | 893 | 3.419e-06 | 0.001497 |
11 | RESPONSE TO ALCOHOL | 4 | 362 | 3.539e-06 | 0.001497 |
12 | CELLULAR RESPONSE TO ORGANIC SUBSTANCE | 6 | 1848 | 3.983e-06 | 0.00152 |
13 | PROTEIN PHOSPHORYLATION | 5 | 944 | 4.497e-06 | 0.00152 |
14 | POSITIVE REGULATION OF EPITHELIAL CELL MIGRATION | 3 | 103 | 4.574e-06 | 0.00152 |
15 | EMBRYONIC ORGAN DEVELOPMENT | 4 | 406 | 5.58e-06 | 0.001731 |
16 | RESPONSE TO ABIOTIC STIMULUS | 5 | 1024 | 6.712e-06 | 0.001735 |
17 | REGULATION OF ANATOMICAL STRUCTURE MORPHOGENESIS | 5 | 1021 | 6.616e-06 | 0.001735 |
18 | CELLULAR RESPONSE TO ENDOGENOUS STIMULUS | 5 | 1008 | 6.212e-06 | 0.001735 |
19 | POSITIVE REGULATION OF VASCULATURE DEVELOPMENT | 3 | 133 | 9.869e-06 | 0.002417 |
20 | MORPHOGENESIS OF AN EPITHELIAL FOLD | 2 | 15 | 1.1e-05 | 0.002443 |
21 | PLACENTA DEVELOPMENT | 3 | 138 | 1.102e-05 | 0.002443 |
22 | RESPONSE TO STEROID HORMONE | 4 | 497 | 1.243e-05 | 0.002534 |
23 | TRANSMEMBRANE RECEPTOR PROTEIN TYROSINE KINASE SIGNALING PATHWAY | 4 | 498 | 1.252e-05 | 0.002534 |
24 | DIGESTIVE SYSTEM DEVELOPMENT | 3 | 148 | 1.36e-05 | 0.002637 |
25 | REGULATION OF REACTIVE OXYGEN SPECIES METABOLIC PROCESS | 3 | 152 | 1.473e-05 | 0.002742 |
26 | TISSUE MORPHOGENESIS | 4 | 533 | 1.638e-05 | 0.002823 |
27 | PHOSPHORYLATION | 5 | 1228 | 1.638e-05 | 0.002823 |
28 | EMBRYO DEVELOPMENT ENDING IN BIRTH OR EGG HATCHING | 4 | 554 | 1.907e-05 | 0.002975 |
29 | REGULATION OF EPITHELIAL CELL MIGRATION | 3 | 166 | 1.918e-05 | 0.002975 |
30 | CELLULAR RESPONSE TO HORMONE STIMULUS | 4 | 552 | 1.88e-05 | 0.002975 |
31 | EMBRYONIC HEMOPOIESIS | 2 | 20 | 1.989e-05 | 0.002986 |
32 | POSITIVE REGULATION OF MULTICELLULAR ORGANISMAL PROCESS | 5 | 1395 | 3.057e-05 | 0.004445 |
33 | RESPONSE TO ENDOGENOUS STIMULUS | 5 | 1450 | 3.692e-05 | 0.005205 |
34 | REGULATION OF RESPONSE TO STRESS | 5 | 1468 | 3.921e-05 | 0.005366 |
35 | RESPONSE TO ESTROGEN | 3 | 218 | 4.329e-05 | 0.005755 |
36 | REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER IN RESPONSE TO HYPOXIA | 2 | 32 | 5.182e-05 | 0.006698 |
37 | REGULATION OF NUCLEOTIDE CATABOLIC PROCESS | 2 | 36 | 6.578e-05 | 0.008272 |
38 | CELLULAR RESPONSE TO OXYGEN CONTAINING COMPOUND | 4 | 799 | 8.034e-05 | 0.009438 |
39 | ERBB2 SIGNALING PATHWAY | 2 | 39 | 7.733e-05 | 0.009438 |
40 | NEGATIVE REGULATION OF DEVELOPMENTAL PROCESS | 4 | 801 | 8.113e-05 | 0.009438 |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|
1 | ENZYME BINDING | 7 | 1737 | 3.686e-08 | 3.425e-05 |
2 | KINASE ACTIVITY | 5 | 842 | 2.558e-06 | 0.001188 |
3 | PROTEIN PHOSPHATASE BINDING | 3 | 120 | 7.245e-06 | 0.001683 |
4 | TRANSFERASE ACTIVITY TRANSFERRING PHOSPHORUS CONTAINING GROUPS | 5 | 992 | 5.741e-06 | 0.001683 |
5 | PHOSPHATASE BINDING | 3 | 162 | 1.783e-05 | 0.003313 |
6 | PROTEIN KINASE ACTIVITY | 4 | 640 | 3.366e-05 | 0.005212 |
7 | UBIQUITIN LIKE PROTEIN LIGASE BINDING | 3 | 264 | 7.653e-05 | 0.009606 |
8 | CYTOKINE RECEPTOR BINDING | 3 | 271 | 8.272e-05 | 0.009606 |
Num | GO | Overlap | Size | P Value | Adj. P Value |
---|
Num | Pathway | Pathview | Overlap | Size | P Value | Adj. P Value |
---|---|---|---|---|---|---|
1 | HIF_1_signaling_pathway_hsa04066 | 4 | 100 | 2.036e-08 | 1.059e-06 | |
2 | FoxO_signaling_pathway_hsa04068 | 3 | 132 | 9.647e-06 | 0.0002508 | |
3 | Jak_STAT_signaling_pathway_hsa04630 | 3 | 162 | 1.783e-05 | 0.000309 | |
4 | Focal_adhesion_hsa04510 | 3 | 199 | 3.298e-05 | 0.0003914 | |
5 | Regulation_of_actin_cytoskeleton_hsa04810 | 3 | 208 | 3.763e-05 | 0.0003914 | |
6 | PI3K_Akt_signaling_pathway_hsa04151 | 3 | 352 | 0.0001795 | 0.001556 | |
7 | Adherens_junction_hsa04520 | 2 | 72 | 0.0002653 | 0.001971 | |
8 | ErbB_signaling_pathway_hsa04012 | 2 | 85 | 0.0003697 | 0.002403 | |
9 | Sphingolipid_signaling_pathway_hsa04071 | 2 | 118 | 0.000711 | 0.004108 | |
10 | Autophagy_animal_hsa04140 | 2 | 128 | 0.0008357 | 0.004346 | |
11 | Signaling_pathways_regulating_pluripotency_of_stem_cells_hsa04550 | 2 | 139 | 0.0009843 | 0.004653 | |
12 | Phospholipase_D_signaling_pathway_hsa04072 | 2 | 146 | 0.001085 | 0.004702 | |
13 | Cellular_senescence_hsa04218 | 2 | 160 | 0.001301 | 0.005204 | |
14 | cAMP_signaling_pathway_hsa04024 | 2 | 198 | 0.001982 | 0.007362 | |
15 | Rap1_signaling_pathway_hsa04015 | 2 | 206 | 0.002143 | 0.007429 | |
16 | Ras_signaling_pathway_hsa04014 | 2 | 232 | 0.002708 | 0.0088 | |
17 | Endocytosis_hsa04144 | 2 | 244 | 0.00299 | 0.009145 | |
18 | Cytokine_cytokine_receptor_interaction_hsa04060 | 2 | 270 | 0.003646 | 0.01053 | |
19 | MAPK_signaling_pathway_hsa04010 | 2 | 295 | 0.004336 | 0.01187 |