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-125a-5p | BRCC3 | 0.6 | 0.01023 | 0.16 | 0.30814 | miRanda | -0.13 | 5.0E-5 | NA | |
| 2 | hsa-miR-218-5p | BRCC3 | -0.57 | 0.0552 | 0.16 | 0.30814 | MirTarget; miRNATAP | -0.12 | 0 | NA | |
| 3 | hsa-miR-23b-3p | BRCC3 | -0.25 | 0.1502 | 0.16 | 0.30814 | MirTarget | -0.14 | 0.00084 | NA |
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|
| 1 | TRANSLATIONAL INITIATION | 13 | 146 | 6.693e-19 | 3.114e-15 |
| 2 | MULTI ORGANISM METABOLIC PROCESS | 12 | 138 | 2.386e-17 | 5.552e-14 |
| 3 | ESTABLISHMENT OF PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM | 10 | 104 | 5.205e-15 | 6.458e-12 |
| 4 | VIRAL LIFE CYCLE | 13 | 290 | 5.552e-15 | 6.458e-12 |
| 5 | PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM | 10 | 123 | 2.917e-14 | 2.715e-11 |
| 6 | PROTEIN TARGETING TO MEMBRANE | 10 | 157 | 3.479e-13 | 2.698e-10 |
| 7 | RIBONUCLEOPROTEIN COMPLEX BIOGENESIS | 13 | 440 | 1.146e-12 | 6.751e-10 |
| 8 | NUCLEAR TRANSCRIBED MRNA CATABOLIC PROCESS NONSENSE MEDIATED DECAY | 9 | 118 | 1.161e-12 | 6.751e-10 |
| 9 | PEPTIDE METABOLIC PROCESS | 14 | 571 | 1.597e-12 | 8.257e-10 |
| 10 | AMIDE BIOSYNTHETIC PROCESS | 13 | 507 | 6.82e-12 | 3.174e-09 |
| 11 | INTERSPECIES INTERACTION BETWEEN ORGANISMS | 14 | 662 | 1.161e-11 | 4.501e-09 |
| 12 | SYMBIOSIS ENCOMPASSING MUTUALISM THROUGH PARASITISM | 14 | 662 | 1.161e-11 | 4.501e-09 |
| 13 | CELLULAR AMIDE METABOLIC PROCESS | 14 | 727 | 4.034e-11 | 1.444e-08 |
| 14 | ESTABLISHMENT OF PROTEIN LOCALIZATION TO MEMBRANE | 10 | 264 | 6.15e-11 | 2.044e-08 |
| 15 | RNA CATABOLIC PROCESS | 9 | 227 | 4.205e-10 | 1.304e-07 |
| 16 | RRNA METABOLIC PROCESS | 9 | 255 | 1.174e-09 | 3.413e-07 |
| 17 | ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE | 10 | 361 | 1.294e-09 | 3.542e-07 |
| 18 | PROTEIN LOCALIZATION TO MEMBRANE | 10 | 376 | 1.916e-09 | 4.952e-07 |
| 19 | NCRNA PROCESSING | 10 | 386 | 2.465e-09 | 6.037e-07 |
| 20 | PROTEIN TARGETING | 10 | 406 | 4.001e-09 | 9.309e-07 |
| 21 | RIBOSOME BIOGENESIS | 9 | 308 | 6.124e-09 | 1.357e-06 |
| 22 | CELLULAR MACROMOLECULAR COMPLEX ASSEMBLY | 12 | 727 | 7.713e-09 | 1.631e-06 |
| 23 | MACROMOLECULE CATABOLIC PROCESS | 13 | 926 | 1.094e-08 | 2.213e-06 |
| 24 | ORGANONITROGEN COMPOUND BIOSYNTHETIC PROCESS | 13 | 1024 | 3.606e-08 | 6.99e-06 |
| 25 | NCRNA METABOLIC PROCESS | 10 | 533 | 5.271e-08 | 9.81e-06 |
| 26 | PROTEIN LOCALIZATION TO ORGANELLE | 10 | 556 | 7.825e-08 | 1.4e-05 |
| 27 | CELLULAR CATABOLIC PROCESS | 14 | 1322 | 8.938e-08 | 1.485e-05 |
| 28 | FORMATION OF TRANSLATION PREINITIATION COMPLEX | 4 | 22 | 8.803e-08 | 1.485e-05 |
| 29 | ORGANIC CYCLIC COMPOUND CATABOLIC PROCESS | 9 | 427 | 1.018e-07 | 1.633e-05 |
| 30 | MACROMOLECULAR COMPLEX ASSEMBLY | 14 | 1398 | 1.786e-07 | 2.77e-05 |
| 31 | REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER IN RESPONSE TO HYPOXIA | 4 | 32 | 4.267e-07 | 6.405e-05 |
| 32 | ORGANONITROGEN COMPOUND METABOLIC PROCESS | 15 | 1796 | 5.898e-07 | 8.576e-05 |
| 33 | MEMBRANE ORGANIZATION | 11 | 899 | 7.501e-07 | 0.0001027 |
| 34 | SINGLE ORGANISM CELLULAR LOCALIZATION | 11 | 898 | 7.419e-07 | 0.0001027 |
| 35 | ESTABLISHMENT OF PROTEIN LOCALIZATION | 13 | 1423 | 1.6e-06 | 0.0002127 |
| 36 | INTRACELLULAR PROTEIN TRANSPORT | 10 | 781 | 1.768e-06 | 0.0002286 |
| 37 | MRNA METABOLIC PROCESS | 9 | 611 | 2.04e-06 | 0.0002566 |
| 38 | RIBONUCLEOPROTEIN COMPLEX SUBUNIT ORGANIZATION | 6 | 199 | 2.233e-06 | 0.0002735 |
| 39 | RNA PROCESSING | 10 | 835 | 3.219e-06 | 0.0003745 |
| 40 | CATABOLIC PROCESS | 14 | 1773 | 3.159e-06 | 0.0003745 |
| 41 | PROTEIN UBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS | 5 | 134 | 6.006e-06 | 0.0006816 |
| 42 | PROTEIN POLYUBIQUITINATION | 6 | 243 | 7.053e-06 | 0.0007814 |
| 43 | REGULATION OF DNA TEMPLATED TRANSCRIPTION IN RESPONSE TO STRESS | 4 | 67 | 8.661e-06 | 0.0009372 |
| 44 | NUCLEOTIDE EXCISION REPAIR DNA DUPLEX UNWINDING | 3 | 22 | 1.029e-05 | 0.001088 |
| 45 | NUCLEOTIDE EXCISION REPAIR DNA DAMAGE RECOGNITION | 3 | 23 | 1.182e-05 | 0.001222 |
| 46 | REGULATION OF TRANSLATIONAL INITIATION | 4 | 82 | 1.935e-05 | 0.001958 |
| 47 | PROTEIN LOCALIZATION | 13 | 1805 | 2.177e-05 | 0.002155 |
| 48 | POSTTRANSCRIPTIONAL REGULATION OF GENE EXPRESSION | 7 | 448 | 2.234e-05 | 0.002165 |
| 49 | NUCLEOTIDE EXCISION REPAIR PREINCISION COMPLEX ASSEMBLY | 3 | 29 | 2.419e-05 | 0.002297 |
| 50 | GLOBAL GENOME NUCLEOTIDE EXCISION REPAIR | 3 | 32 | 3.27e-05 | 0.003043 |
| 51 | DNA DAMAGE RESPONSE DETECTION OF DNA DAMAGE | 3 | 36 | 4.681e-05 | 0.004189 |
| 52 | POSITIVE REGULATION OF ERBB SIGNALING PATHWAY | 3 | 36 | 4.681e-05 | 0.004189 |
| 53 | VIRION ASSEMBLY | 3 | 37 | 5.088e-05 | 0.004467 |
| 54 | NUCLEOTIDE EXCISION REPAIR DNA INCISION | 3 | 39 | 5.968e-05 | 0.005142 |
| 55 | POSITIVE REGULATION OF LIGASE ACTIVITY | 4 | 110 | 6.142e-05 | 0.005196 |
| 56 | NUCLEOTIDE EXCISION REPAIR | 4 | 113 | 6.822e-05 | 0.005668 |
| 57 | PROTEOLYSIS | 10 | 1208 | 7.9e-05 | 0.006449 |
| 58 | CELLULAR MACROMOLECULE LOCALIZATION | 10 | 1234 | 9.439e-05 | 0.007573 |
| 59 | REGULATION OF LIGASE ACTIVITY | 4 | 130 | 0.0001175 | 0.009268 |
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|
| 1 | STRUCTURAL CONSTITUENT OF RIBOSOME | 9 | 212 | 2.293e-10 | 2.13e-07 |
| 2 | RNA BINDING | 14 | 1598 | 9.13e-07 | 0.0004241 |
| 3 | TRANSLATION INITIATION FACTOR ACTIVITY | 4 | 51 | 2.888e-06 | 0.0008942 |
| 4 | POLY A RNA BINDING | 11 | 1170 | 9.617e-06 | 0.001787 |
| 5 | STRUCTURAL MOLECULE ACTIVITY | 9 | 732 | 8.865e-06 | 0.001787 |
| 6 | TRANSLATION FACTOR ACTIVITY RNA BINDING | 4 | 89 | 2.675e-05 | 0.004142 |
| Num | GO | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|
| 1 | CYTOSOLIC RIBOSOME | 9 | 113 | 7.803e-13 | 4.557e-10 |
| 2 | RIBOSOMAL SUBUNIT | 9 | 163 | 2.183e-11 | 6.375e-09 |
| 3 | RIBOSOME | 9 | 226 | 4.044e-10 | 5.904e-08 |
| 4 | CYTOSOLIC PART | 9 | 223 | 3.592e-10 | 5.904e-08 |
| 5 | RIBONUCLEOPROTEIN COMPLEX | 13 | 721 | 5.332e-10 | 6.228e-08 |
| 6 | EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX | 4 | 16 | 2.209e-08 | 1.843e-06 |
| 7 | TRANSLATION PREINITIATION COMPLEX | 4 | 16 | 2.209e-08 | 1.843e-06 |
| 8 | CYTOSOLIC LARGE RIBOSOMAL SUBUNIT | 5 | 61 | 1.187e-07 | 8.665e-06 |
| 9 | LARGE RIBOSOMAL SUBUNIT | 5 | 95 | 1.102e-06 | 7.148e-05 |
| 10 | CYTOSOLIC SMALL RIBOSOMAL SUBUNIT | 4 | 44 | 1.584e-06 | 9.251e-05 |
| 11 | SMALL RIBOSOMAL SUBUNIT | 4 | 68 | 9.189e-06 | 0.0004878 |
| 12 | NUCLEAR UBIQUITIN LIGASE COMPLEX | 3 | 42 | 7.466e-05 | 0.003634 |
Over-represented Pathway
| Num | Pathway | Pathview | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|---|
| 1 | Oocyte_meiosis_hsa04114 | 3 | 124 | 0.001806 | 0.09393 | |
| 2 | Cell_cycle_hsa04110 | 2 | 124 | 0.02433 | 0.6326 |
