FDR control by the BH procedure for two-sided correlated tests with implications to gene expression data analysis

The multiple testing problem attributed to gene expression analysis is challenging not only by its size, but also by possible dependence between the expression levels of different genes resulting from coregulations of the genes. Furthermore, the measurement errors of these expression levels may be dependent as well since they are subjected to several technical factors. Multiple testing of such data faces the challenge of correlated test statistics. In such a case, the control of the False Discovery Rate (FDR) is not straightforward, and thus demands new approaches and solutions that will address multiplicity while accounting for this dependency. This paper investigates the effects of dependency between bormal test statistics on FDR control in two-sided testing, using the linear step-up procedure (BH) of Benjamini and Hochberg (1995). The case of two multiple hypotheses is examined first. A simulation study offers primary insight into the behavior of the FDR subjected to different levels of correlation and distance between null and alternative means. A theoretical analysis follows in order to obtain explicit upper bounds to the FDR. These results are then extended to more than two multiple tests, thereby offering a better perspective on the effect of the proportion of false null hypotheses, as well as the structure of the test statistics correlation matrix. An example from gene expression data analysis is presented.     

Robust control of nitrogen assimilation by a bifunctional enzyme in E. coli

Bacteria regulate the assimilation of multiple nutrients to enable growth. How is balanced utilization achieved, despite fluctuations in the concentrations of the enzymes that make up the regulatory circuitry? Here we address this question by studying the nitrogen system of E. coli. A mechanism based on the avidity of a bifunctional enzyme, adenylyltransferase (AT/AR), to its multimeric substrate, glutamine synthetase, is proposed to maintain a robust ratio between two key metabolites, glutamine and α-ketoglutarate. This ratio is predicted to be insensitive to variations in protein levels of the core circuit and to the rate of nitrogen utilization. We find using mass spectrometry that the metabolite ratio is robust to variations in protein levels and that this robustness depends on the bifunctional enzyme. Moreover, robustness carries through to the bacteria growth rate. Interrupting avidity by adding a monofunctional AT/AR mutant to the native system abolishes robustness, as predicted by the proposed mechanism.     

Increased Cyclic AMP-Dependent Protein Kinase Activity in Postmortem Brain from Patients with Bipolar Affective Disorder

Previous observations of reduced [3H]cyclic AMP binding in postmortem brain regions from bipolar affective disorder subjects imply cyclic AMP-dependent protein kinase function may be altered in this illness. To test this hypothesis, basal and stimulated cyclic AMP-dependent protein kinase activity was determined in cytosolic and particulate fractions of postmortem brain from bipolar disorder patients and matched controls. Maximal enzyme activity was significantly higher (104%) in temporal cortex cytosolic fractions from bipolar disorder brain compared with matched controls. In temporal cortex particulate fractions and in the cytosolic and particulate fractions of other brain regions, smaller but statistically nonsignificant increments in maximal enzyme activity were detected. Basal cyclic AMP-dependent protein kinase activity was also significantly higher (40%) in temporal cortex cytosolic fractions of bipolar disorder brain compared with controls. Estimated EC50 values for cyclic AMP activation of this kinase were significantly lower (70 and 58%, respectively) in both cytosolic and particulate fractions of temporal cortex from bipolar disorder subjects compared with controls. These findings suggest that higher cyclic AMP-dependent protein kinase activity in bipolar disorder brain may be associated with a reduction of regulatory subunits of this enzyme, reflecting a possible adaptive response of this transducing enzyme to increased cyclic AMP signaling in this disorder.     

Ejaculation Induced by the Activation of Crz Neurons Is Rewarding to Drosophila Males

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Protein Tyrosine Phosphatase Inhibitors in FcγRI-Induced Myeloid Oxidant Signaling

Fc-receptor stimulation in myeloid cells results in increased oxygen consumption, termed the respiratory burst, which is coupled to a rapid and transient increase in tyrosine phosphorylation of cellular proteins. In a previous paper in this journal we showed that the protein tyrosine phosphatase (PTPase) inhibitors sodium orthovanadate and phenylarsine oxide (PAO) block the FcγRI-induced respiratory burst in interferon-γ-differentiated U937 cells (U937IF) while augmenting the FcγRI-induced tyrosine phosphorylation of cellular proteins. Herein we examine the effects of PTPase inhibitors on specific molecules involved in FcγRI signaling. We show that orthovanadate and PAO augmented the FcγRI-induced tyrosine phosphorylation of the adaptor protein CBL. CBL interactions with other phosphoproteins, among them SHC and CRKL, were also augmented in response to pretreatment with the PTPase inhibitors. SHC was tyrosine phosphorylated in response to FcγRI stimulation of U937IF cells and bound to the SH2 domain of GRB2 in a stimulation-dependent manner. In fusion protein pull-down experiments the interaction of SHC with the SH2 domain of GRB2 was increased in PTPase inhibitor pretreated U937IF cells in response to FcγRI stimulation. Our data support the hypothesis that a tyrosine dephosphorylation event is required for effective transmission of the FcγRI signal to result in activation of the myeloid respiratory burst response.