The most fundamental 3-deazaneplanocin A-Competition

gondii genes as the early node on the phylogenetic tree where the most distant species have genes with significant sequence homology (reciprocal BLASTP E value find more co-expression relationships, the organisms from whom transcriptomes are sampled must be exposed to various growth conditions. This approach has been successfully used in other eukaryotes (Stuart et al., 2003; Hu et al., 2010; Mutwil et al., 2011). For Chromera, we generated RNA-seq-based transcriptome under combinations of varying salt concentrations, iron concentrations, and temperature changes, resulting in 36 unique combinations (see ��Materials and methods�� and Figure 4��figure supplement 1C). For P. falciparum, we obtained previously published microarray-based gene expression data sets of 144 unique conditions Ro3280 from 23 time series, representing stresses from various growth-inhibiting compounds (Hu et al., 2010). It has been shown that gene expression data generated using different molecular platforms are reproducible and accurate enough for cross-platform comparisons (Woo et al., 2004). Based on each data set, we calculated Spearman correlation coefficients rho between all possible pairs from the 1918 orthogroups shared between Chromera and P. falciparum (1918 �� 1918 matrix). We also calculated a 1918 �� 1918 weighted adjacency matrix using CLR algorithm (Faith et al., 2007) as implemented in an R package minet (with parameters of method = ��clr��, estimator = ��mi.shrink��, and disc = ��equalfreq��) (Meyer et al., 2008). Expression level of multiple genes in a given orthogroup was averaged. To rule 3-deazaneplanocin A datasheet out any potential systematic biases associated with averaging expression levels of homologous, yet distinct genes, we repeated some of the analyses with 1560 orthogroups that have one-to-one orthologs between the two species and reached the same conclusions (data not shown). A pair of genes (or orthogroup) were determined as co-expressed if the Spearman's correlation coefficient rho is greater than 0.3 and if the value from the weighted adjacency matrix of the network is greater than 0.01. We calculated an odds-ratio to measure the extent of conservation of co-expressed genes: (# of genes co-expressed in both species) �� (# of genes co-expressed in none of the species)/([# of genes co-expressed in P. falciparum only] �� [# of genes co-expressed in C.