HUMAN Downloads

The human transcriptome data used in this work have been downloaded from the repository of the FANTOM5 project (http://fantom.gsc.riken.jp/5/). FANTOM is an international research consortium that generates and shares high-quality transcriptome datasets (CC BY 4.0)
The raw FANTOM5 dataset amounts to 1829 samples, encompassing human cell lines (271), primary cells (564) and tissues (188) also part of time course experiments (785) and fractionations/perturbations (21). FANTOM5 identified 201802 distinct genomic transcription start site (TSS) locations, corresponding to bona-fide transcript isoforms. A first filtering has been applied on the dataset to exclude unknown transcripts, i.e. without an annotated HGNC symbol (https://www.genenames.org/). This step resulted in a collection of 87554 transcripts, associated with 18889 genes, constituting our full version of the dataset (FANTOM-full)” (Blanzieri et. al. https://ieeexplore.ieee.org/document/9224179)

The list of 87554 isoforms present in the transcriptomic data set.

OneGenE is a method to compute ranked candidate gene lists that expands known local gene networks given gene expression data. As its predecessor NES2RA, OneGenE  is based on the systematic and iterative application of the skeleton function of the PC algorithm on subsets of the input data. OneGenE aims to overcome the large latency of NES2RA when applied to LGNs, by pre-computing partial results, namely single-gene NES2RA expansions, on the BOINC platform.
(Blanzieri et. al. https://ieeexplore.ieee.org/document/9224179)

The single-gene NES2RA expansions of FANTOM-full were submitted on the BOINC platform, with a tile size of 1000 transcripts, 1000 iterations and 0.05 as alpha threshold. The output as presented here is a list of pair of transcripts with the absolute and relative frequency of detection the latter while expanding the gene regulatory network of the former.

The values of Pearson correlation computed on the transcriptomic dataset above.

The same of Pearson data but limited to the pair who has a non zero relative frequency in the OneGenE data.