To assign Functional Associations by Response Overlap (FARO) between an experimental factor and the factors assessed in a compendium of gene expression responses, a query response of differentially expressed genes from one study was compared to the responses of the compendium (Figure 1).
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
In addition, we used a compendium of gene synonyms and aliases to improve recall.
By comparing the result of mpk4 versus wild type gene expression to a compendium of Arabidopsis gene expression responses, we identified associations to a meaningful subset of experimental factors within the compendium.
This chapter is a compendium of facts, challenges and opportunities in the characterization of biomedical polymers.
A likely C. briggsae orthologue was sought for each gene in the compendium of C. elegans transcription factor genes we generated recently [ 15].
The survey was developed as a compendium of instruments, assessing demographic factors, sexual behaviors, discrimination and stigma, sex work, sexual partnerships and social support.
As a test of the approach, we determined FARO of the Arabidopsis MAP kinase 4 loss of function mutant (mpk4) against a compendium of 241 Arabidopsis gene expression profiles representing responses to experimental factors.
For example, a compendium of environmental and growth factor-induced perturbations could be employed to develop an objective compatible with these procedures.
This book is not a compendium of bacterial toxins and virulence factors but rather a selection of molecular mechanisms of host-parasite interaction.
Similarly, no linkage between these factors was observed in a compendium of deletion mutants, where both gene expression and growth rate were modified not by changing an environment but rather by deleting specific genes.
