Explanation
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-223-3p | ACSL3 | -0.97 | 0 | 0.18 | 0.04159 | MirTarget | -0.14 | 0 | NA | |
| 2 | hsa-miR-223-3p | ADCY1 | -0.97 | 0 | -0.05 | 0.84149 | mirMAP | -0.38 | 0 | NA | |
| 3 | hsa-miR-223-3p | ADM2 | -0.97 | 0 | 2.41 | 0 | mirMAP | -0.16 | 8.0E-5 | NA | |
| 4 | hsa-miR-223-3p | ALCAM | -0.97 | 0 | 0.51 | 0.00106 | MirTarget | -0.29 | 0 | NA | |
| 5 | hsa-miR-223-3p | ANTXR1 | -0.97 | 0 | -0.18 | 0.16983 | mirMAP | -0.11 | 0.00023 | NA | |
| 6 | hsa-miR-223-3p | AR | -0.97 | 0 | -1 | 0.00094 | mirMAP | -0.55 | 0 | 21453483 | miR 223 regulates migration and invasion by targeting Artemin in human esophageal carcinoma; To develop potential therapy targeting ARTN we studied the roles of miR-223 in the migration and invasion of human esophageal carcinoma; ARTN mRNA contains a binding site for miR-223 in the 3'UTR; Co-transfection of a mir-223 expression vector with pMIR-ARTN led to the reduced activity of luciferase in a dual-luciferase reporter gene assay suggesting that ARTN is a target gene of miR-223; Overexpression of miR-223 decreased expression of ARTN in KYSE150 cells while silencing miR-223 increased expression of ARTN in EC9706 cells; These results reveal that ARTN a known tumor metastasis-related gene is a direct target of miR-223 and that miR-223 may have a tumor suppressor function in esophageal carcinoma and could be used in anticancer therapies |
| 7 | hsa-miR-223-3p | ARTN | -0.97 | 0 | 3.04 | 0 | miRNAWalker2 validate; miRTarBase | -0.16 | 0.00543 | 21453483 | miR 223 regulates migration and invasion by targeting Artemin in human esophageal carcinoma; To develop potential therapy targeting ARTN we studied the roles of miR-223 in the migration and invasion of human esophageal carcinoma; ARTN mRNA contains a binding site for miR-223 in the 3'UTR; Co-transfection of a mir-223 expression vector with pMIR-ARTN led to the reduced activity of luciferase in a dual-luciferase reporter gene assay suggesting that ARTN is a target gene of miR-223; Overexpression of miR-223 decreased expression of ARTN in KYSE150 cells while silencing miR-223 increased expression of ARTN in EC9706 cells; These results reveal that ARTN a known tumor metastasis-related gene is a direct target of miR-223 and that miR-223 may have a tumor suppressor function in esophageal carcinoma and could be used in anticancer therapies |
| 8 | hsa-miR-223-3p | ATP7A | -0.97 | 0 | -0.47 | 0 | MirTarget | -0.15 | 0 | NA | |
| 9 | hsa-miR-223-3p | CBX5 | -0.97 | 0 | 0 | 0.95384 | MirTarget | -0.13 | 0 | NA | |
| 10 | hsa-miR-223-3p | CCDC96 | -0.97 | 0 | 0.93 | 0 | MirTarget | -0.24 | 0 | NA | |
| 11 | hsa-miR-223-3p | CDK17 | -0.97 | 0 | -0.12 | 0.11999 | MirTarget | -0.14 | 0 | NA | |
| 12 | hsa-miR-223-3p | CXXC4 | -0.97 | 0 | -0.35 | 0.08009 | MirTarget | -0.34 | 0 | NA | |
| 13 | hsa-miR-223-3p | DDI2 | -0.97 | 0 | -0.87 | 0 | mirMAP | -0.14 | 0.00174 | NA | |
| 14 | hsa-miR-223-3p | E2F1 | -0.97 | 0 | 2.6 | 0 | miRNAWalker2 validate; miRTarBase | -0.14 | 0.00034 | 20029046 | Cell cycle regulator E2F1 and microRNA 223 comprise an autoregulatory negative feedback loop in acute myeloid leukemia; In this report we demonstrate that during granulopoiesis microRNA-223 targets E2F1; E2F1 protein was up-regulated in miR-223 null mice; Our study supports a molecular network involving miR-223 C/EBPalpha and E2F1 as major components of the granulocyte differentiation program which is deregulated in AML |
| 15 | hsa-miR-223-3p | ECT2 | -0.97 | 0 | 1.65 | 0 | MirTarget | -0.18 | 0 | 24784921; 23601845 | MicroRNA-223 miR-223 has been demonstrated to be implicated in cell proliferation and cell cycle progression of osteosarcoma cell lines by regulating its target gene epithelial cell transforming sequence 2 ECT2; To address this problem we firstly showed that the expression levels of miR-223 and Ect2 messenger RNA were respectively down-regulated and up-regulated in osteosarcoma tissues compared with those in noncancerous bone tissues significantly both P < .001 according to the results of quantitative real-time reverse transcription-polymerase chain reaction; Notably miR-223 down-regulation was negatively correlated with Ect2 messenger RNA up-regulation in osteosarcoma tissues r = -0.68 P = .01; Then the combined low miR-223 expression and high Ect2 expression miR-223-low/Ect2-high was significantly associated with high tumor grade P = .01 poor response to chemotherapy P = .01 positive metastasis P < .001 and recurrence P < .001 of osteosarcomas; In conclusion our data offer convincing evidence that the deregulation of miR-223 and its target gene ECT2 may be associated with the aggressive tumor progression of human osteosarcoma; Of note the combined miR-223 down-regulation and Ect2 up-regulation may be a possible marker of poor prognosis in this malignancy;Further mechanistic study indicated that Ect2 was directly targeted by miR-223; Downregulation of Ect2 by miR-223 induces the expression of p21 p27 and the phospharylation of retinoblastoma which are involved in the G1 block |
| 16 | hsa-miR-223-3p | FAM199X | -0.97 | 0 | 0.25 | 0.00094 | MirTarget | -0.16 | 0 | NA | |
| 17 | hsa-miR-223-3p | GABRB2 | -0.97 | 0 | -0.41 | 0.05864 | mirMAP | -0.31 | 0 | NA | |
| 18 | hsa-miR-223-3p | GLYR1 | -0.97 | 0 | 0.48 | 0 | mirMAP | -0.11 | 0 | NA | |
| 19 | hsa-miR-223-3p | HARBI1 | -0.97 | 0 | 0.67 | 0 | MirTarget | -0.12 | 0 | NA | |
| 20 | hsa-miR-223-3p | HOOK1 | -0.97 | 0 | 1.27 | 0 | MirTarget | -0.34 | 0 | NA | |
| 21 | hsa-miR-223-3p | IGF1R | -0.97 | 0 | 0.12 | 0.48217 | miRNAWalker2 validate; miRTarBase; MirTarget | -0.33 | 0 | NA | |
| 22 | hsa-miR-223-3p | IL6ST | -0.97 | 0 | -1.53 | 0 | MirTarget | -0.22 | 0.00038 | NA | |
| 23 | hsa-miR-223-3p | IPO9 | -0.97 | 0 | 0.55 | 0 | mirMAP | -0.11 | 0 | NA | |
| 24 | hsa-miR-223-3p | IQCE | -0.97 | 0 | 0.74 | 0 | mirMAP | -0.11 | 0 | NA | |
| 25 | hsa-miR-223-3p | KCNC1 | -0.97 | 0 | -0.42 | 0.12578 | mirMAP | -0.27 | 5.0E-5 | NA | |
| 26 | hsa-miR-223-3p | KCND3 | -0.97 | 0 | -1.65 | 0 | mirMAP | -0.18 | 0.00622 | NA | |
| 27 | hsa-miR-223-3p | KSR2 | -0.97 | 0 | -0.09 | 0.65861 | mirMAP | -0.38 | 0 | NA | |
| 28 | hsa-miR-223-3p | LRIG1 | -0.97 | 0 | -0.62 | 0 | MirTarget | -0.19 | 0 | NA | |
| 29 | hsa-miR-223-3p | MAP3K9 | -0.97 | 0 | 0.5 | 3.0E-5 | mirMAP | -0.15 | 0 | NA | |
| 30 | hsa-miR-223-3p | MARCH10 | -0.97 | 0 | 1.82 | 0 | MirTarget | -0.46 | 0 | NA | |
| 31 | hsa-miR-223-3p | MMP16 | -0.97 | 0 | -0.48 | 0.0113 | mirMAP | -0.2 | 1.0E-5 | NA | |
| 32 | hsa-miR-223-3p | MTSS1 | -0.97 | 0 | 0.27 | 0.02255 | MirTarget | -0.18 | 0 | NA | |
| 33 | hsa-miR-223-3p | NIPA1 | -0.97 | 0 | 0.39 | 0 | mirMAP | -0.15 | 0 | NA | |
| 34 | hsa-miR-223-3p | NUP210 | -0.97 | 0 | 2.1 | 0 | MirTarget | -0.19 | 0 | NA | |
| 35 | hsa-miR-223-3p | PARD6B | -0.97 | 0 | 1.71 | 0 | MirTarget | -0.44 | 0 | NA | |
| 36 | hsa-miR-223-3p | PARP1 | -0.97 | 0 | 1.14 | 0 | miRNAWalker2 validate | -0.12 | 0 | NA | |
| 37 | hsa-miR-223-3p | PTPRT | -0.97 | 0 | -0.92 | 0.01369 | mirMAP | -0.41 | 0 | NA | |
| 38 | hsa-miR-223-3p | RAB11FIP4 | -0.97 | 0 | 1.53 | 0 | mirMAP | -0.24 | 0 | NA | |
| 39 | hsa-miR-223-3p | RALGPS1 | -0.97 | 0 | 0.32 | 0.00074 | mirMAP | -0.24 | 0 | NA | |
| 40 | hsa-miR-223-3p | RALGPS2 | -0.97 | 0 | 0.89 | 0 | MirTarget | -0.33 | 0 | NA | |
| 41 | hsa-miR-223-3p | RASA1 | -0.97 | 0 | -0.29 | 0.00077 | MirTarget | -0.11 | 0 | 25867276 | C/EBP β activated microRNA 223 promotes tumour growth through targeting RASA1 in human colorectal cancer; The levels of RASA1 and miR-223 were analysed by real-time PCR western blotting or in situ immunofluorescence analyses; Upregulation of miR-223 was detected in CRC tissues P<0.01 and was involved in downregulation of RASA1 in CRC tissues; Furthermore the direct inhibition of RASA1 translation by miR-223 and the activation of miR-223 by CCAAT/enhancer binding protein-β C/EBP-β were evaluated in CRC cells; These results identify that C/EBP-β-activated miR-223 contributes to tumour growth by targeting RASA1 in CRC and miR-223-targeted inhibitors may have clinical promise for CRC treatment via suppression of miR-223 |
| 42 | hsa-miR-223-3p | RERG | -0.97 | 0 | -0.48 | 0.0125 | MirTarget | -0.32 | 0 | NA | |
| 43 | hsa-miR-223-3p | RHOB | -0.97 | 0 | -0.17 | 0.14825 | miRNAWalker2 validate; miRTarBase; MirTarget | -0.12 | 3.0E-5 | NA | |
| 44 | hsa-miR-223-3p | RIBC1 | -0.97 | 0 | 1.03 | 0 | MirTarget | -0.33 | 0 | NA | |
| 45 | hsa-miR-223-3p | RNF14 | -0.97 | 0 | -0.02 | 0.67605 | MirTarget | -0.13 | 0 | NA | |
| 46 | hsa-miR-223-3p | RPS6KB1 | -0.97 | 0 | -0.06 | 0.49809 | MirTarget | -0.14 | 0 | NA | |
| 47 | hsa-miR-223-3p | SAMD12 | -0.97 | 0 | 0.75 | 0 | mirMAP | -0.26 | 0 | NA | |
| 48 | hsa-miR-223-3p | SLC1A2 | -0.97 | 0 | 0.46 | 0.04286 | mirMAP | -0.46 | 0 | NA | |
| 49 | hsa-miR-223-3p | SLC46A1 | -0.97 | 0 | -0.31 | 0.00251 | mirMAP | -0.19 | 0 | NA | |
| 50 | hsa-miR-223-3p | SRP54 | -0.97 | 0 | 0.59 | 0 | MirTarget | -0.17 | 0 | NA | |
| 51 | hsa-miR-223-3p | SSBP2 | -0.97 | 0 | -0.69 | 0 | MirTarget | -0.11 | 0 | NA | |
| 52 | hsa-miR-223-3p | STK39 | -0.97 | 0 | 0.35 | 0.00163 | MirTarget | -0.14 | 0 | NA | |
| 53 | hsa-miR-223-3p | TRIL | -0.97 | 0 | -0.09 | 0.49347 | MirTarget | -0.18 | 0 | NA | |
| 54 | hsa-miR-223-3p | TWF1 | -0.97 | 0 | 0.31 | 1.0E-5 | MirTarget | -0.14 | 0 | NA | |
| 55 | hsa-miR-223-3p | UBE2W | -0.97 | 0 | 0.22 | 0.00401 | mirMAP | -0.12 | 0 | NA | |
| 56 | hsa-miR-223-3p | UBR5 | -0.97 | 0 | -0.07 | 0.35955 | MirTarget | -0.1 | 0 | NA | |
| 57 | hsa-miR-223-3p | ULK2 | -0.97 | 0 | -0.38 | 3.0E-5 | MirTarget | -0.12 | 0 | NA | |
| 58 | hsa-miR-223-3p | VPS13B | -0.97 | 0 | -0.13 | 0.17494 | mirMAP | -0.15 | 0 | NA | |
| 59 | hsa-miR-223-3p | VPS52 | -0.97 | 0 | 0.41 | 0 | mirMAP | -0.11 | 0 | NA | |
| 60 | hsa-miR-223-3p | WDR26 | -0.97 | 0 | 0.21 | 0.00037 | mirMAP | -0.12 | 0 | NA | |
| 61 | hsa-miR-223-3p | XPR1 | -0.97 | 0 | 0.23 | 0.00588 | MirTarget | -0.12 | 0 | NA | |
| 62 | hsa-miR-223-3p | ZFHX3 | -0.97 | 0 | -0.35 | 0.00018 | MirTarget | -0.2 | 0 | NA | |
| 63 | hsa-miR-223-3p | ZNF365 | -0.97 | 0 | 0.54 | 0.00043 | MirTarget | -0.17 | 0 | NA | |
| 64 | hsa-miR-223-3p | ZNF587 | -0.97 | 0 | 0.62 | 0 | mirMAP | -0.28 | 0 | NA | |
| 65 | hsa-miR-223-3p | ZNF772 | -0.97 | 0 | -0.23 | 0.04969 | MirTarget | -0.13 | 1.0E-5 | 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 |
|---|---|---|---|---|---|
| 1 | CELL SURFACE | 12 | 757 | 5.05e-06 | 0.002949 |
Over-represented Pathway
| Num | Pathway | Pathview | Overlap | Size | P Value | Adj. P Value |
|---|---|---|---|---|---|---|
| 1 | Oocyte_meiosis_hsa04114 | 3 | 124 | 0.007682 | 0.1703 | |
| 2 | Autophagy_animal_hsa04140 | 3 | 128 | 0.008379 | 0.1703 | |
| 3 | Signaling_pathways_regulating_pluripotency_of_stem_cells_hsa04550 | 3 | 139 | 0.01048 | 0.1703 | |
| 4 | mTOR_signaling_pathway_hsa04150 | 3 | 151 | 0.0131 | 0.1703 | |
| 5 | Rap1_signaling_pathway_hsa04015 | 3 | 206 | 0.0295 | 0.2931 | |
| 6 | Ras_signaling_pathway_hsa04014 | 3 | 232 | 0.03979 | 0.2931 | |
| 7 | HIF_1_signaling_pathway_hsa04066 | 2 | 100 | 0.04199 | 0.2931 | |
| 8 | Endocytosis_hsa04144 | 3 | 244 | 0.04509 | 0.2931 | |
| 9 | AMPK_signaling_pathway_hsa04152 | 2 | 121 | 0.059 | 0.3409 | |
| 10 | Apelin_signaling_pathway_hsa04371 | 2 | 137 | 0.07327 | 0.381 | |
| 11 | MAPK_signaling_pathway_hsa04010 | 2 | 295 | 0.2489 | 0.6718 | |
| 12 | PI3K_Akt_signaling_pathway_hsa04151 | 2 | 352 | 0.3176 | 0.6718 |
