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Evolutionary conservation and regulatory potential are the most informative additional data source in our simulations, whereas estimated nucleosome locations or CpG-islands do not improve TF binding predictions.
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Therefore, these suboptimal HCs were omitted from further analyses, reducing the final data set from 126,996 reads to 123,003 most informative HCs (Additional file 1, Table S4).
The input features related to evolutionary information were consistently most informative for SNAP2 (Additional File 1, Fig. SOM_1: SNAP2 vs. SNAP2noali).
Identification of both of these classic biomarkers of prostate carcinomas (PSA and KLK2), in our list of the most informative genes, provides additional evidence to the hypothesis that functional connectivity changes and not only differential expression levels are highly correlated to normal/tumoral process.
For the non coding SNPs, both the Evanno's test and the Kruskal Wallis analysis of the log-likelihood variance indicated that the most informative K was 7 (Additional file 7: Figure S1c and S1d).
For finer mapping, a series of D9Dcr primers (the most informative primers are listed below, additional markers in the interval can be found on the Mouse Genome Informatics website - www.informatics.jax.org/) were designed using Ensembl sequence such that primer pairs spanned regions of dinucleotide repeats.
Histograms of the beta value distribution at 30 most informative loci are given in Additional file 2: Figure S1.> -wrap-foot> Pofition of CpG residue according to Genome Build 37. Heterozygosity as reported by UCSC Genome Browser.
In order to recommend a useful subset of SNPs for routine genetic diversity and mapping studies in tropical and sub-tropical maize germplasm (those related to the materials in this study) using uniplex assays, we chose 644 of the most informative and repeatable SNPs (listed in Additional file 2: Table S2).
For multipoint analysis of larger linkage groups we used the option BUILD to select loci to be used as a framework for the continuing ordering of them, beginning with the most informative pair of markers and positioning additional markers one at a time in order of decreasing informativeness; the order of selected markers, also called framework loci, was supported by a LOD score of three or higher.
The phyletic retention measure was, as in yeast, found to be the most informative feature when ranking by conditional mutual information [ Additional file 1].
We conducted data decay analysis to obtain additional insight into the most informative attributes.
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