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elisabettasciacca / DEGGs

Differentially Expressed Gene-Gene pairs
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gene-gene interaction network #3

Closed ghost closed 2 years ago

ghost commented 2 years ago

Hi Elisabetta

Can i clarify with you if the network used from the curated network mentioned in the manuscript or derived from the dataset?

Thank you.

elisabettasciacca commented 2 years ago

Hi kengcher,

Sorry this is not clear from the preprint because you don't have access to supplementary material. Networks are derived starting from an extensive network of 10’537 molecular interactions obtained from KEGG, mirTARbase, miRecords and transmiR (this was curated in Alaimo et al. 2016 doi:10.18632/oncotarget.9788). To extract group-specific subnetworks, two filtering steps are done. First, nodes not reaching high average levels of expression are removed, then a second filtering stage removes common interactions across groups.

Do let me know if this makes sense or of you need further explanaitions!

Elisabetta

ks2022ml commented 2 years ago

Hi Elisabetta

Thank you for the clarification!

3 additional questions:

  1. Is the default network the metapathway_gene_symbols with 40,252 gene-gene interactions (although in the preprint it's mentioned that the network has 10,537 experimentally evaluated gene-gene interactions)

  2. Would you kindly point me to which part of the code the metapathway_gene_symbols is loaded?

  3. is the resulting subnetwork directed as print_force_network seems to suggest so with arrows in the edges.

Thank you very much!

elisabettasciacca commented 2 years ago

Hi,

Sorry, for some reason I missed this message.

Regarding your questions:

  1. The reason why the metapathway_gene_symbols network contains so many interactions is due to an old implementation of the package. For each interaction we had a third column indicating the type of link (inhibition or activation, info taken from KEGG). When a link was acting as both inhibitor and activator two entries were shown, one per type. Since we are not using this information anyomore I could actually remove the redundant links, I'll do it in the next commit.

  2. The network is loaded at lines 90, 101 (when gene symbols are selected) and 113 (for entrez IDs)

  3. Yes, the pathways in KEGG are directed so we kept this directionality

Hope this can help, Elisabetta