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Most of these procedures exploits other kinds of data in addition to expression data, e.g. counts of regulatory motifs that serve as binding sites for transcription factors [47], [48], or ChIP-based binding data [49].
Such analyses can be used to augment traditional approaches prior to initiating laboratory experiments but can also elucidate details of protein function and potentially lead to information regarding the origin of proteins and motifs that serve particular functions, protein interrelationships and/or pathway evolution.
Enhancers are expected to be enriched for motifs that serve as putative TF binding sites.
ESEs are short (6 8 nucleotides long) exonic motifs that serve as binding sites for specific serine/arginine-rich proteins [ 30].
The C-terminal p6 region of the viral Gag structural protein contains canonical PTAP and YPXnL motifs that serve as the major functional late assembly domains in most cell types.
By combining the structural analysis with the microevolutionary analysis of WSP, we can speculate that the extracellular loops contain peptide motifs that serve to evade or inhibit host detection, aiding in the early settlement and persistence of Wolbachia into a new host.
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Both Hsp70 and Hsp90 feature a C-terminal EEVD motif that serves as acceptor site for cochaperones that harbour a tetratricopeptide repeat (TPR) domain [12].
Most Fbw7 substrates contain a phosphodegron motif that serves as the recognition motif for Fbw7 interaction (Welcker and Clurman, 2008).
RhoH contains a novel ITAM-like motif that serves as a binding site for Zap70, which is then shuttled to the T-cell receptor complex where it serves as a crucial molecule to trigger activation of the LAT signalosome.
Additionally, all CY and ER homologs possess the R-A-[KR]-F-E-E-L consensus motif that serves as a potential signature for eukaryotic non-organellar Hsp70 proteins [ 35].
One of the most recognized functions of the CSN is the deneddylation of the cullin-RING-ubiquitin ligase (CRL) and this function is reliant on the Jab1 MPN domain metalloenzyme (JAMM) motif that serves as the catalytic center [ 5, 6].
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