The two-dye array compendium consisted of 229 drug treatment samples [ 5]; 208 drug treatments, environmental stresses, and substrate depletions (unpublished); and an additional 53 samples representing an in vitro life cycle time course experiment [ 4].
First, the original training compendium of RMA-normalized Affymetrix data was used to infer the gene-gene interaction network B. This training compendium consisted of 1039 Affymetrix YG S98 GeneChips, representing 465 experimental conditions [ 12].
A large multi data set compendium consisting of 165 diverse data sets (see Additional file 3: Table S3) was used to generate an accurate representation of gene expression.
The sequence compendium consists of 9 aligned fasta files, one for each of HIV-1's proteins.
Recently, Pagliarini et al. [3]undertook a systematic identification of mitochondrially localized proteins using a combination of mass spectrometry, GFP tagging, and computational methods to create a protein compendium consisting of 1098 mitochondrial mammalian proteins.
Because RMT ensures only highly significant interactions are kept, the GIL compendium consists of 558,022 unique high quality A. thaliana co-expression relationships across almost all of the measurable genes on the ATH1 array.
As benchmarks we used not only the DREAM4 In Silico Network challenge but also a novel and unprecedented synthetic compendium consisting of several realistic 5000-gene networksimulateded with varying biological and measurement error variances resulting in a total of 270 datasets.
We used two different case studies for benchmarking: (i) the datasets of the DREAM4 Inetwork_Sinferencetwork inferenchallengenge, and (ii) a novel large-scale synthetic compendium consisting of 30 5000-gene networks simulated by SysGenSIM [ 41] with different connectivities and noise levels.
To compare the new methods with existing ones we not only apply them to a recent DREAM network inference challenge but also to a novel and unprecedented synthetic compendium consisting of 30 5000-gene networks simulated with varying biological and measurement error variances resulting in a total of 270 datasets.
The questionnaire consisted of 26 items selected from the Compendium of Respiratory Standard Questionnaire for adults, which was chosen because of its high internal consistency and reliability.
The development team, dubbed Kajar Laboratories, primarily consisted of members of the Chrono fansite Chrono Compendium.
