Paton, V. | Search bioRxiv

bioRxiv2024

NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks

SummaryWe present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage and evaluation. NetworkCommons aims to be an infrastructure for the network biology community that supports the development of better methods and benchmarks, by enhancing interoperability and integration. Availability and ImplementationNetworkCommons is implemented in Python and offers programmatic access to multiple omics datasets, network inference methods, and benchmarking setups. It is a free software, available at https://github.com/saezlab/networkcommons. Contactsaezlab@ebi.ac.uk, martin.garrido@embl.de Supplementary DataContribution guidelines, additional figures, and descriptions for data, knowledge, methods, evaluation strategies and their implementation are available in the Supplementary Data and in the NetworkCommons documentation at https://networkcommons.readthedocs.io/.

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bioRxiv2023

Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results

Transcriptomics, and in particular RNA-Seq, has become a widely used approach to assess the molecular state of biological systems. To facilitate its analysis, many tools have been developed for different steps, such as filtering lowly expressed genes, normalisation, differential expression, and enrichment. While numerous studies have examined the impact of method choices on differential expression results, little attention has been paid to their effects on further downstream functional analysis using enrichment of gene sets, such as pathways, which typically provides the basis for interpretation and follow-up experiments. To address this gap, we introduce FLOP (FunctionaL Omics Processing), a comprehensive nextflow-based workflow that combines various methods for preprocessing and downstream enrichment analysis, allowing users to perform end-to-end analyses of count level transcriptomic data. We illustrate FLOP capabilities on diverse datasets comprising samples from end-stage heart failure patients and cancer cell lines in both basal and drug-perturbed states. We found that the correlation between gene set enrichment analysis results can vary significantly for alternative pipelines. Additionally, we observed that not filtering the data had the highest impact on the correlation between pipelines in the gene set space, especially in settings with limited statistical power. Overall, our results underscore the impact of carefully evaluating the consequences of the choice of preprocessing methods on downstream enrichment analyses. We envision FLOP as a valuable tool to measure the robustness of functional analyses, ultimately leading to more reliable and conclusive biological findings. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=45 SRC="FIGDIR/small/557538v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@1b35ee7org.highwire.dtl.DTLVardef@11bd02aorg.highwire.dtl.DTLVardef@ff7b18org.highwire.dtl.DTLVardef@ea8d2c_HPS_FORMAT_FIGEXP M_FIG C_FIG

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