In this study, we have developed a novel framework to quantify the roles of different types of biases in influencing the genome-wide ChIP-seq signal using a large compendium of ENCODE datasets.
Although numerous previous works have considered mappability as a factor influencing read densities [ 15, 19, 22], and chromatin accessibility is known to influence transcription factor binding [ 20], our analysis provides systematic confirmation and quantification of these influences using a large compendium of ENCODE datasets.
We used a large compendium of mRNA signatures derived from cells treated with drugs to investigate the mechanism of action of CG-mediated cytotoxicity [24].
Thus, by using a larger expression compendium, S-MAP was able to expand the number of individual genes implicated in stemness beyond the one gene, Itga6, identified by the original founder studies.
In some cases, global co-expression networks are created using a large number of samples from publicly available repositories the goal being to mine knowledge across the compendium of samples not previously identified through individual experiments.
In order to account for the dynamic properties of proteins as well as their dynamic relationship with their neighbors in the network, we used gene expression information from a large compendium of microarray data and a high quality collection of protein interaction data to derive 9 network metrics that describe the dynamic behavior of a protein and of its neighborhood in the network (see Methods).
To generate hypotheses regarding the mechanism of action, we used the Connectivity Map (CMAP) [18], which is a large compendium of gene expression signatures from drug-treated cell lines.
In a study by Hughes and coworkers [ 14], a large compendium of yeast gene expression data was examined for co‐expression patterns using hierarchical clustering and among several findings, they discovered that a previously unannotated gene, YER044c (now ERG28), had a gene expression pattern that was highly similar to genes that were known to be involved in ergosterol biosynthesis.
A large compendium of gene expression datasets, which covers about 466 growth conditions, was used for the analysis.
The term was combined with enkyklios ("complete system," or "circle") to identify a large compendium of general education, hence "encyclopaedia".
However, these studies were all based on a large compendium [4] which was not controlled for systematic errors such as sampling rate.
