• Replicability in gene function prediction

    Replicability in gene network analysis Networks Networks are constructed based upon (i.) protein-protein interactions, (ii.) semantic similarity, and (iii.) co-expression. The co-expression networks are very dense. Please contact us if you are interested in the complete network (threshold is used to reduce the connectivity). Protein-protein interaction BioGRID: network and robustness analysis: updated network HIPPIE: network IntAct: network and robustness analysis: updated network […]
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  • Functional effect size trend

    SUPPLEMENTARY MATERIALS GENE SETS We have made the gene sets used in the study available here as a R binary files. https://github.com/sarbal/EffectSize/blob/master/asd_gene_sets.Rdata https://github.com/sarbal/EffectSize/blob/master/all_gene_sets.Rdata https://github.com/sarbal/EffectSize/blob/master/gwas.combined.Rdata DISEASE PROPERTIES We have made the different disease gene properties used in the study available as an R binary file. These are the scores of individual genes (if available). https://github.com/sarbal/EffectSize/blob/master/all.rank.properties.Rdata   […]
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  • RNA-seq networks

    SUPPLEMENTARY MATERIALS Guidance for RNA-seq co-expression network construction and analysis: safety in numbers  NETWORK DATA We have made thresholded versions of the aggregate networks described in the paper available in R. eg, load(<file.Rdata>) NETWORK CONSTRUCTION Each aggregate network is the average of individual co-expression networks, built from individual expression based experiments (i.e., a tissue transcriptome, […]
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  • Aggregate gene function prediction

    Aggregate gene function prediction Supplementary figures Benchmarking ‘off-the-shelf’ machine learning algorithms with participants of the MouseFunc critical assessment. (A) The performance of the submission in the MouseFunc critical assessment. The biological processes from the gene ontology with three intervals of functional annotations are used to compare the performance of the participants. The participants were A […]
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