[Apr 6th 2022] LabMeeting: Swim: a computational tool to unveiling crucial nodes in complex biological networks.

Elia Giuseppe Ceroni (University of Siena)

When: Apr 6th, 2022 – 11:00 – 11:45 AM
Where: Google meet link
Description

Swim: a computational tool to unveiling crucial nodes in complex biological networks.

SWItchMiner (SWIM) is a wizard-like software implementation of a procedure[1] capable to extract information contained in complex networks, developed by Paci et al.[2].Specifically, SWIM allows unearthing the existence of a new class of hubs, called “fight-club hubs”, characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called “switch genes”, appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance.
In this meeting I will describe how SWIM works and report the result obtained by the authors when they applied the tool to the expression profiling of glioblastoma stem-like cells and conventional glioma cell lines [3].

References:
[1] Palumbo, M.C., Zenoni, S., Fasoli, M., Massonnet, M., Farina, L., Castiglione, F., Pezzotti, M., Paci, P., Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development , The Plant Cell, Volume 26, Issue 12, December 2014, Pages 4617–4635, https://doi.org/10.1105/tpc.114.133710
[2] Paci, P., Colombo, T., Fiscon, G. et al. SWIM: a computational tool to unveiling crucial nodes in complex biological networks. Sci Rep 7, 44797 (2017). https://doi.org/10.1038/srep44797
[3] Fiscon, G., Conte, F., & Paci, P. (2018). SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines. BMC bioinformatics, 19(Suppl 15), 436. https://doi.org/10.1186/s12859-018-2421-x

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