Phillips and Kinser have attracted a set of deeply thoughtful authors in this nuanced compendium of competing analyses and perspectives.
Applied to this large compendium of data sets, meta-analyses demonstrated that conserved patterns between species could be identified.
For survival analyses, the compendium of gene expression array data sets of breast cancer was previously compiled, with subtypes assigned as described elsewhere.
Given the dominant role of transcriptional regulation in ESC function (Jaenisch and Young, 2008; Nichols and Smith, 2012; Niwa, 2007; Smith, 2009; Young, 2011) we generated a compendium of transcription factor ChIP-seq analyses (see Figures S1A and S1B and Table S1 available online and http://bioinformatics.cscr.cam.ac.uk/ES_Cell_ChIP-seq_compendium.html).html
We foresee that such a compendium for widespread analysis will facilitate these types of analyses on a far larger scale.
We have investigated macrophage activation using computational analyses of a compendium of transcriptomic data covering responses to agonists of the TLR pathway, Salmonella infection, and manufactured amorphous silica nanoparticle exposure.
This system biology project is a comprehensive compendium of transcriptomic, proteomic, metabolomic and ionomic analyses from maize grown under a large set of controlled stress conditions (drought, cold, nutrient deficit) or developmental stages (Colmsee et al. 2012).
Together, our compendium and analyses provide a first step toward the characterization of RBP regulatory networks in C. elegans and serve as a model for the continued study of RBPs in other organisms, including humans.
For all our motif enrichment analyses we used a compendium of 884 motifs ("JASPAR+Jolma compendium") that we created by combining all vertebrate motifs from JASPAR [ 23] with all the SELEX-based motifs from [ 3].
This RNA-Seq compendium extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing [ 29, 31, 32].
