We chose the differentiation pathway towards erythroid cells for further investigation because (i) the pathway is well characterized at the experimental level; (ii) it has been the subject of modelling approaches based on simple two-gene interactions (Chickarmane et al., 2009; Roeder and Glauche, 2006); and (iii) it connects two stable states in our modelling based on our 11 gene network.
We developed a broadly applicable, platform-independent and clinically relevant method based on simple ratios of gene expression to diagnose human cancers.
Model-based meta-analysis approaches can rise above seemingly weak consistency among studies based on simple comparison of lists of genes.
First, only nodes that have related gene profiles (based on partial correlations), as distinguished from all indirectly related gene profiles (based on simple correlations), are connected in the network (see B below).
It should also be considered that the eight-gene classifier was obtained by a multivariate algorithm and preselection of probe sets based on individual variances, whereas the consensus list is based on simple overlap analysis of all genes up- or down-regulated by all HDACi.
These 'molecular scissors' have allowed a cheaper, faster and more accurate alternative to traditional gene targeting based on simple homologous recombination.
We did not find any explanation for incorrect gene essentiality predictions based on simple statistics such as rudimentary network size metrics.
To best use phenotypic class information to our advantage, we define our informativeness metric based on simple ANOVA statistics that come from comparing gene expression profiles between phenotypic groups and which is, therefore, focused on differences between groups rather than differences within groups.
The gene pairs were selected based on simple pairwise comparisons between two marker expression levels within the same sample.
Genic microsatellites are those microsatellites based on simple sequence repeats (SSRs) found within, or closely associated with, gene sequences from a given genome [ 1].
