Third, uncertainty of existing land use intensity metrics is often high (e.g. due to positional inaccuracy, unreliable input data, or processing algorithms limitations), as highlighted by the large discrepancies of alternative global cropland extent maps [ 50 ] or fertilizer application maps [ 8,51], and remain largely unquantified, because formal validation is often lacking.
We then used the BLASTP output and positional information as input for MCScanX (Wang et al. 2012), used with default values, to detect homologous chromosomal regions between human and platypus (supplementary table S3, Supplementary Material online) and human and chicken (supplementary table S4, Supplementary Material online).
In addition, PscanChIP evaluates motif positional bias within the input regions.
Additional information on each motif's positional distribution among the input set is provided (Fig. 1C).
We selected all 2-kB promoter regions and chose positional gene sets as input for the enrichment analysis.
Additional information for each motif is displayed, including its distribution among the input set, positional bias, strand bias and similarity to known motifs.
The accuracy of the results of the proximity analysis technique described above will depend in part on the positional accuracy of the input data [ 49, 55].
Sensory input for positional and egg-laying preferences occurs at Gr66a -expressing neurons in the anterior legs and the pharynx, respectively.
As the analysis in [ 15] was performed on single methylation sites and we did not intent to replicate the analysis, validation was done via an unbiased gene set enrichment analysis using positional gene sets as input.
Positional bias within the input sequences becomes then another key factor for assessing the significance of a motif, as in ref. [ 100] where IC is applied also to the position where motifs appear with respect to a background uniform distribution, or in the HMS tool.
