About


PlanNET is a web application that stores predicted Schmidtea mediterranea protein-protein interactions (ppi) projected over a Human ppi network. Currently, PlanNET holds 273,203 human ppi, and 729,043 Schmidtea mediterranea interactions (predicted for 9 different transcriptomes).

PlanNET has been developed by the Computational Genomics Lab, at the University of Barcelona.



Citing PlanNET

PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
S. Castillo-Lara, J.F. Abril
Bioinformatics, Volume 34, Issue 6, 15 March 2018, Pages 1016–1023, btx738

  • BibTex:
        @article{Castillo-Lara2018,
            author = {Castillo-Lara, S and Abril, J F},
            title = {"PlanNET: homology-based predicted interactome for multiple planarian transcriptomes"},
            journal = {Bioinformatics},
            volume = {34},
            number = {6},
            pages = {1016--1023},
            year = {2018},
            doi = {10.1093/bioinformatics/btx738},
            URL = {http://dx.doi.org/10.1093/bioinformatics/btx738},
            eprint = {/oup/backfile/content_public/journal/bioinformatics/34/6/10.1093_bioinformatics_btx738/2/btx738.pdf}
        }
    


Update Notes

PlanNET has been updated from version 1.0 (published version at Bioinformatics) to version 1.1. These are the most important changes:
  • In order to look for homologous proteins for each planarian transcript, we prioritized BLAST instead of EggNOG alignments.
  • The RandomForest classifier was refined by filtering the training dataset further, removing interactions not annotated as physical from BioGRID.
  • We selected a score cut-off of 0.7 for interactions, instead of the previously used 0.6 cut-off. The Filter Interactions slider in NetExplorer was updated: now it only shows interactions with a score higher than 0.7 by default, but the user can still select other cut-off values
  • PlanNET now holds 729,043 Schmidtea mediterranea interactions (up from 510,996).
  • The Smed454 dataset and Newmark dataset were temporarily removed because of disk size limitations. These will be uploaded in due time.
  • A manually curated list of identifiers for planarian transcripts was uploaded to PlanNET. Now users can search for these identifiers, which follow the form: "Smed_XXX". If a particular transcripts has a manually curated identifier, the identifier will appear in pink both in Gene Search and in the corresponding Gene Card.
  • New Data Downloader allows users to download sequences and sequence annotations in bulk. Available at downloads page.
  • Many quality of life improvements to the overall design of the website, including a search bar in NetExplorer.