ArticleBioinformatics (Oxford, England)2018
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 24 citations in OpenAlex.
- Article
- LIM-HD transcription factors control axial patterning and specify distinct neuronal and intestinal cell identities in planarians.Open biology · 2023Article
- Review
- Wnt/β-catenin signalling is required for pole-specific chromatin remodeling during planarian regeneration.Nature communications · 2023Article
- alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria.International journal of molecular sciences · 2021Article
- WNT-FRIZZLED-LRP5/6 Signaling Mediates Posterior Fate and Proliferation during Planarian Regeneration.Genes · 2021Article
- Article
- The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma.BMC genomics · 2020Article
- Poly(ADP-Ribose) Polymerase-3 Regulates Regeneration in Planarians.International journal of molecular sciences · 2020Article
- Planarian regeneration as a model of anatomical homeostasis: Recent progress in biophysical and computational approaches.Seminars in cell & developmental biology · 2019Review
- RPGeNet v2.0: expanding the universe of retinal disease gene interactions network.Database : the journal of biological databases and curation · 2019Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Planarians are emerging as a model organism to study regeneration in animals. However, the little available data of protein-protein interactions hinders the advances in understanding the mechanisms underlying its regenerating capabilities. Results: We have developed a protocol to predict protein-protein interactions using sequence homology data and a reference Human interactome. This methodology was applied on 11 Schmidtea mediterranea transcriptomic sequence datasets. Then, using Neo4j as our database manager, we developed PlanNET, a web application to explore the multiplicity of networks and the associated sequence annotations. By mapping RNA-seq expression experiments onto the predicted networks, and allowing a transcript-centric exploration of the planarian interactome, we provide researchers with a useful tool to analyse possible pathways and to design new experiments, as well as a reproducible methodology to predict, store, and explore protein interaction networks for non-model organisms. Availability and implementation: The web application PlanNET is available at https://compgen.bio.ub.edu/PlanNET. The source code used is available at https://compgen.bio.ub.edu/PlanNET/downloads. Contact: jabril@ub.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.