In order to place the newly acquired merozoite gene expression in context of the life cycle, the data were analyzed in combination with a recently published dataset by Fritz HM et al. 2012 [ 27] covering day 0, 4, 10 oocyst (array sample names: OD0, OD4, OD10), day 2 tachyzoite (TD2), and day 4, 8, 21 bradyzoite (BD4, BD8, BD21) development.
Interestingly, 238 of the 243 genes were detectable in the control samples of a recently published dataset obtained by ribosomal profiling of Arabidopsis seedlings [ 15], indicating that the genes are translated also in general conditions.
First a recently published dataset of regions bound by a transcriptional regulator are compared to general genomic features and those specific to the cell line of origin, K562.
To further investigate the relation to IM, we performed an additional enrichment analysis compared to a recently published dataset of IM as well as SPEM marker genes, obtained by microarray analysis of microdissected human SPEM and IM tissue [ 16].
We also used a recently published dataset to test performance of our subnetworks.
To take phylogenetic and branch-length uncertainty into account in our analyses, we generated Bayesian trees by combining three recently published datasets [ 34, 36, 39] and confirmed that our phylogeny was consistent with that proposed previously (Additional file 1: Figure S3).
To begin to understand the relation between the core oscillator and the AtGRP7 slave oscillator and their respective downstream transcripts, we monitored recently published datasets for the phase distribution of transcripts controlled by TOC1 and LHY with reference to the Edwards dataset [ 35, 44, 45].
First, we briefly review the pioneering methods that use hand-crafted representations and then we delve in detail into the deep learning-based approaches and recently published datasets.
The comparative analysis of recently published datasets involving human gene expression responses to two bacterial respiratory pathogens illustrates many of these points.
For this purpose, we used three recently published datasets experimentally-derived from two different solar cells libraries.
We evaluated the different approaches on two recently published datasets.
