Schistosoma mansoni lncRNAs Database
Other Cytoscape Networks
The 181 robust lincRNAs (red nodes; lincRNAs from the main intersection in the UpSet Intersection Diagram on Fig. 4 from the Sci. Rep. paper) were used as bait for catching 2,359 PC genes (blue nodes) whose expression levels across five developmental stages are either positively (r ≥ 0.8, cyan edges) or negatively (r ≤ −0.8, gray edges) correlated with the expression levels of the lincRNAs. The network contains 68,625 edges among which 63,156 (92%) are positive correlations and 5,469 (8%) negative ones.
This network is called "pccAll-cor0p8sigpval2net-DEedgeDE-lincSMP-181mainInt.sif" within the cytoscape file "CoexpNetwork-cor0p8-DEedgeDE-lincSMP-181mainInt.cys", which can be downloaded through the green button below.
Complete view of the lincRNA-PC gene co-expression network built by the Topological Filtering Step (TFS) approach.
“Network Analyzer” function from cytoscape was used in order to obtain betweenness centrality score for each node, meaning the bigger the node, the higher propensity to be a hub. The network contains 89 SmLINC nodes (red) and 237 PC gene (Smp) nodes (blue), with 62.5% of positively correlated pairs (204 / 326, r ≥ 0.5, cyan edges) and 37.5% of negatively correlated ones (122 / 326, r ≤ -0.5, gray edges). Dashed edges represent neighbor genes.
This network is called "biclustering-lincSMP-TFS-cor0p5.sif" within the cytoscape file "CoexpNetwork-cor0p8-DEedgeDE-lincSMP-181mainInt.cys", which can be downloaded through the green button below.
Network with 2,965 nodes, 750 lincRNAs (red) + 2,215 PC genes (blue), and 52,913 edges, of which 51,807 are for positive r (cyan) and 1,106 for negative (gray) r correlation coefficient. The network was built by using 307 highly differentially expressed Smps (log2FC ≥ 10 on at least one out of five developmental stages) as bait in order to rescue all the other genes that presented a very stringent expression correlation coefficient (r ≥ 0.9 or r ≤ -0.9) with them.
This network is called "pccAll-cor0p9sigpval2net-SMPlogFCgt10edgeDE.sif" within the cytoscape file "CoexpNetwork-cor0p9-SMPlogFCgt10edgeDE.cys", which can be downloaded through the green button below.