## 5 Discovery of functional relevant TFBSs
### Context-specific search
Specifically, recent studies have shown that genes sharing similar expression patterns can participate in a number of different biological functions and/or genes in the same pathway can exhibit different patterns of expression [122, 123]. Moreover, the underlying gene regulation is shown to be tissue and/or condition specific and the TFs that drive the gene expression are very flexible in function and activity under different conditions [103-106]. Therefore, defining the context in which a set of genes are more likely to be co-regulated poses a formidable challenge to researchers. A number of assumptions have been suggested and preliminary results appear promising. For example, [PERSON] et al. [124] attempted to generate testable hypotheses like'regulator X regulates co-expression module Y under conditions W' with the assumption that co-expressed genes across a set of conditions will be co-regulated. The work was done on yeast with some cases experimentally verifiedsuccessfully. Similarly, [PERSON] et al. [125] analyzed a set of coexpressed gene that are cell-cycle-dependent and found eight TFs whose binding sites are significantly overrepresented in their promoters, or [PERSON] et al. [109] identified statistically overrepresented cooperating TFBSs in the 1 kbp upstream sequence set of each biological-process gene group in GO. **Figure 3**. **(a)** A brief overview of how computational models are developed. Motif discovery methods consist of three main components: the binding site representation, the scoring function, and the search strategy. There are alternative approaches for searching novel motifs, including scanning for TFs with known profiles. Phylo- tools incorporate phylogenetic relationships among species or their corresponding promoter sequences, and the binding site evolution model to improve the search strategies. Besides, context-specific information can also be explored to predict functional binding sites and then infer a set of context-relevant TFs for further analysis. **(b)** Different strategies to predict _cis_-regulatory elements using additional biological knowledge. Two main strategies exist: single gene, multiple species and single motif discovery methods vs. multiple genes, single species and _cis_-regulatory module discovery methods. The concept of _cis_-regulatory modules was introduced to capture the biological aspect as well as enhance the specificity of the search, especially in higher organisms; besides, other combinatorial strategies have also been developed in the literature (dash arrows). Besides the two main strategies for discovery functional binding sites, i.e. single gene, multiple species, single motifs for detecting general functional binding sites; and multiple genes, single species, composite motifs plus context for predicting context-specific functional binding sites as well as relevant condition-specific activated TFs, other combinatorial strategies have also been developed in the literature. For example, combining co-expressed genes with phylogenetic footprinting for single motif discovery [87, 126-128] or for composite motif discovery [129]. On the other hand, some studies require a collection of promoter sequences with known module sites to serve as training data for building predictive models [130-133]. These approaches seem to be more accurate both in detecting single TFBSs [42, 46] and in predicting TF-modules [132, 133]. However, these models have to be built carefully, cannot be easily inferred automatically, and a number of parameters need to be determined using training data.