A strategy overlooking pedigree error, in the interest of maximising pedigree links, may not be optimal as pedigree errors may also be associated with low power in upstream analyses (i.e. estimation of heritability [ 16]).
Comparative analyses of upstream regions in Toxoplasma gondii, a more distant apicomplexan does not reveal the presence of the same conserved motifs in the groups studied (data not shown).
The analyses of putative upstream regulatory elements showed both shared and distinct transcriptional regulation motifs of ZmLTPs, further indicating that ZmLTPs may play roles in diverse biological processes.
To perform analyses of TIS upstream regions, annotations of TISs were collected from the database ProTISA [ 39] or predicted by TriTISA [ 40].
MEME-based analyses of the upstream regions of all genes overexpressed by at least 4-fold under iron limitation identified a motif bearing strong similarity to the FUR binding sites of E. coli and Pseudomonas spp. [ 33].
The analyses of putative upstream regulatory elements further indicated that ZmLTPs may be involved in diverse biological processes and provided new insights into the shared and different transcriptional regulation machineries of ZmLTPs.
The analyses of putative upstream regulatory elements by two approaches further support the functions of subfamily A in ABA signaling, and provide insights into the shared and different transcriptional regulation machineries in dicots and monocots.
CpG islands in the vicinity of the NAT genes (Matas et al., 1997) and their murine equivalents (Fakis et al., 2000) indicate methylation sites and analyses of the upstream spliced region show this is the case (Kim et al., 2008; Wakefield et al., 2010).
While the gene-coding region of the four OXO genes have >90% nucleotide identity, analyses of their 1,000-bp 1,000-bp regions within Nipponbare show little nupstreame identity, which may affect how duplicate genes function in naturegions
In silico (MatInspector) analyses of genomic sequence upstream of the TSSs defined by 5'-RACE failed to identify a TATA box.
