Summary of the comparison. Boldface indicates significantly better performance than the other methods (including equal top performance).

<p>Summary of the comparison. Boldface indicates significantly better performance than the other methods (including equal top performance).</p

Properties of the tested methods.

<p>Properties of the tested methods.</p

Similarity between methods.

<p>(A) For each pair of methods, the Euclidean distance between the PWMs of the two methods is reported. Before the comparison, the column method's PWM is trimmed to eight most informative contiguous positions. (B–D) ranking based comparisons. For each pair of methods, the probe ranking defined according to the column's method is used as reference, and the ranking of the row's method is evaluated using AUC (B) and sensitivity at 1% false positive (C). In (D), for each pair of methods, the 4σ positive sets of the paired PBM are first ranked by each method, and the Spearman rank coefficient of those rankings is computed. In all tables, the average over 230 PBM experiments is reported. Red colour corresponds to greater similarity.</p

Examples of generated motifs.

<p>The figure shows examples of the motifs produced by each method and the corresponding JASPAR motif. For three proteins, the PWM logos produced by each method and the experimentally and independently established motif in the JASPAR database are shown. AM was trained on motif length 8, while for BE, RM and SW only the most informative contiguous positions were kept. We chose TFs whose motifs had information content most similar to the averages of the different methods.</p

Similarity to experimentally established PWMs.

<p>For 58 TFs, we compared the motifs produced from their PBM profiles by each method, to the known motif from JASPAR database. Distance was measured using Euclidean distance. Three distance cutoffs were used, and the fraction of recovered motifs with distance below the cutoff is the success rate. BE: BEEML-PBM, RM: RankMotif++, SW: Seed-and-Wobble, AM: Amadeus-PBM, JR: JASPAR.</p

Test data and evaluation criteria.

<p>The table lists the data and evaluation criteria used in each benchmark.</p

Functional genomic delineation of TLR-induced transcriptional networks-2

<p><b>Copyright information:</b></p><p>Taken from "Functional genomic delineation of TLR-induced transcriptional networks"</p><p>http://www.biomedcentral.com/1471-2164/8/394</p><p>BMC Genomics 2007;8():394-394.</p><p>Published online 29 Oct 2007</p><p>PMCID:PMC2175519.</p><p></p>puted for three disjoint sets of genes – putative targets of each single element separately (604 NF-κB targets, 838 ISRE targets), and targets of both elements (55 genes), obtained by scanning the promoters of all the genes in the MmBMM dataset. Y-axis is average logof induction fold relative to time 0. Genes whose promoters contain hits for both NF-κB and ISRE elements were more strongly induced by LPS than genes whose promoters contain a hit for only one of these two elements

Functional genomic delineation of TLR-induced transcriptional networks-1

<p><b>Copyright information:</b></p><p>Taken from "Functional genomic delineation of TLR-induced transcriptional networks"</p><p>http://www.biomedcentral.com/1471-2164/8/394</p><p>BMC Genomics 2007;8():394-394.</p><p>Published online 29 Oct 2007</p><p>PMCID:PMC2175519.</p><p></p>into three kinetic sets according to the time their expression was first induced and the time it peaked. The 'EE' set contains the early induction, early peak genes; the 'ED' set contains early induction, delayed peak genes; and the 'DD' set contains delayed induction, delayed peak genes. The figure displays the mean expression patterns of the genes assigned to the three kinetic sets in the MmBMM dataset (y-axis is logof induction fold). (B) Mean expression of induced genes that encode for TFs: ATF/CREB (Atf3, Fos, Jun, Junb), NF-κB (Nfkb1, Nfkb2, Rel, Relb), and ISRE (Irf1, Irf2, Irf7, Stat1, Stat2, Stat3, Stat5a). The expression pattern of each TF is highly correlated with that of the kinetic wave, in which the computational promoter analysis found an over-representation of its BSs (compare the kinetic expression of the TF genes (B) and the induced waves (A))

Functional genomic delineation of TLR-induced transcriptional networks-3

<p><b>Copyright information:</b></p><p>Taken from "Functional genomic delineation of TLR-induced transcriptional networks"</p><p>http://www.biomedcentral.com/1471-2164/8/394</p><p>BMC Genomics 2007;8():394-394.</p><p>Published online 29 Oct 2007</p><p>PMCID:PMC2175519.</p><p></p>mulators (induction of at least 1.8-fold at any time point) were partitioned into distinct sets according to their agent-induction pattern. Taking into account sets that contained at least 40 genes, only two complex induction patterns were identified in addition to the six agent-specific patterns: universal and LPS-PIC patterns. Selected genes are shown in the heat-map for each set (a complete list of genes is provided in Additional File ). The maximum induction of the gene over the examined time points per stimulator is depicted in the heat-map. (B) Enriched GO functional categories were identified in the universal and LPS-PIC sets (-values in parentheses are corrected for multiple testing using a bootstrap procedure on 1,000 randomly chosen gene sets of the same size as the true sets). (C) Highly significant over-represented cis-regulatory elements were identified in the promoters of the universal and LPS-PIC sets, pointing to a pivotal role for NF-κB and ISRE in the induction of these two components of the TLR-induced transcriptional program

Functional genomic delineation of TLR-induced transcriptional networks-0

<p><b>Copyright information:</b></p><p>Taken from "Functional genomic delineation of TLR-induced transcriptional networks"</p><p>http://www.biomedcentral.com/1471-2164/8/394</p><p>BMC Genomics 2007;8():394-394.</p><p>Published online 29 Oct 2007</p><p>PMCID:PMC2175519.</p><p></p>mulators (induction of at least 1.8-fold at any time point) were partitioned into distinct sets according to their agent-induction pattern. Taking into account sets that contained at least 40 genes, only two complex induction patterns were identified in addition to the six agent-specific patterns: universal and LPS-PIC patterns. Selected genes are shown in the heat-map for each set (a complete list of genes is provided in Additional File ). The maximum induction of the gene over the examined time points per stimulator is depicted in the heat-map. (B) Enriched GO functional categories were identified in the universal and LPS-PIC sets (-values in parentheses are corrected for multiple testing using a bootstrap procedure on 1,000 randomly chosen gene sets of the same size as the true sets). (C) Highly significant over-represented cis-regulatory elements were identified in the promoters of the universal and LPS-PIC sets, pointing to a pivotal role for NF-κB and ISRE in the induction of these two components of the TLR-induced transcriptional program