Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

Motivation: Recently, many univariate and several multivariate approaches have been suggested for testing differential expression of gene sets between different phenotypes. However, despite a wealth of literature studying their performance on simulated and real biological data, still there is a need to quantify their relative performance when they are testing different null hypotheses.

Results: In this article, we compare the performance of univariate and multivariate tests on both simulated and biological data. In the simulation study we demonstrate that high correlations equally affect the power of both, univariate as well as multivariate tests. In addition, for most of them the power is similarly affected by the dimensionality of the gene set and by the percentage of genes in the set, for which expression is changing between two phenotypes. The application of different test statistics to biological data reveals that three statistics (sum of squared t-tests, Hotelling's T2, N-statistic), testing different null hypotheses, find some common but also some complementing differentially expressed gene sets under specific settings. This demonstrates that due to complementing null hypotheses each test projects on different aspects of the data and for the analysis of biological data it is beneficial to use all three tests simultaneously instead of focusing exclusively on just one.

The absence of creativity in Feist and the computational process

The decision of the U.S. Supreme Court in 1991 in Feist Publications, Inc. v. Rural Tel. Service Co. affirmed originality as a constitutional requirement for copyright. Originality has a specific sense and is constituted by a minimal degree of creativity and independent creation. The not original is the more developed concept within the decision. It includes the absence of a minimal degree of creativity as a major constituent. Different levels of absence of creativity also are distinguished, from the extreme absence of creativity to insufficient creativity. There is a gestalt effect of analogy between the delineation of the not original and the concept of computability. More specific correlations can be found within the extreme absence of creativity. "[S]o mechanical" in the decision can be correlated with an automatic mechanical procedure and clauses with a historical resonance with understandings of computability as what would naturally be regarded as computable. The routine within the extreme absence of creativity can be regarded as the product of a computational process. The concern of this article is with rigorously establishing an understanding of the extreme absence of creativity, primarily through the correlations with aspects of computability. The understanding established is consistent with the other elements of the not original. It also revealed as testable under real-world conditions. The possibilities for understanding insufficient creativity, a minimal degree of creativity, and originality, from the understanding developed of the extreme absence of creativity, are indicated. 

Revealing differences in gene network inference algorithms on the network level by ensemble methods

Motivation: The inference of regulatory networks from large-scale expression data holds great promise because of the potentially causal interpretation of these networks. However, due to the difficulty to establish reliable methods based on observational data there is so far only incomplete knowledge about possibilities and limitations of such inference methods in this context.

Results: In this article, we conduct a statistical analysis investigating differences and similarities of four network inference algorithms, ARACNE, CLR, MRNET and RN, with respect to local network-based measures. We employ ensemble methods allowing to assess the inferability down to the level of individual edges. Our analysis reveals the bias of these inference methods with respect to the inference of various network components and, hence, provides guidance in the interpretation of inferred regulatory networks from expression data. Further, as application we predict the total number of regulatory interactions in human B cells and hypothesize about the role of Myc and its targets regarding molecular information processing.