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Pipeline publication

[…] with <2000 bp between the transcriptional start sites (TSS). Co-expressed gene clusters were defined as >5 contiguous genes with expression data displaying a Pearson’s Correlation Coefficient of >0.5 with neighbouring genes. Cluster co-expression data was visualized with corrplot and Cytoscape (v3.1.0), location of related clusters was visualized by Circos. Gene expression periodicity was measured on 120 interpolated expression values for each replicate time series using GeneCycle, candidate periodically expressed genes were identified as having the same calculated dominant cycling frequency between biological replicates. Time-dependent expression signatures were established using maSigPro with a replicate correlation coefficient cutoff of 0.8. Target genes of potential regulatory (top 50 most highly and/or variably expressed) lncRNAs were identified using the GeneReg package on 100 point-interpolated expression data based on fitted expression values between duplicates and setting a maximum time delay of 18 hours and a global correlation coefficient of 0.9 and visualized using Cytoscape. Gene lists were functionally annotated with KEGG and Reactome pathways (adjusted p value < 0.05) using the clusterProfiler and ReactomePA packages., Data has been deposited into GEO under accession number GSE75028., , Electronic supplementary material , Supplementary information accompanies this paper at doi:10.1038/s41598-017-06110-5 , Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations., The authors acknowledge Kenneth Sabir and Ruth Pidsley for reviewing the manuscript; the Garvan Foundation and the Peter Wills Bioinformatics Facility for providing facilities and Agilent Technologies for […]

Pipeline specifications

Software tools maSigPro, GeneReg, Cytoscape