A first principles approach to differential expression in microarray data analysis

<p>Abstract</p> <p>Background</p> <p>The disparate results from the methods commonly used to determine differential expression in Affymetrix microarray experiments may well result from the wide variety of probe set and probe level models employed. Here we take the approach of making the fewest assumptions about the structure of the microarray data. Specifically, we only require that, under the null hypothesis that a gene is not differentially expressed for specified conditions, for any probe position in the gene's probe set: a) the probe amplitudes are independent and identically distributed over the conditions, and b) the distributions of the replicated probe amplitudes are amenable to classical analysis of variance (ANOVA). Log-amplitudes that have been standardized within-chip meet these conditions well enough for our approach, which is to perform ANOVA across conditions for each probe position, and then take the median of the resulting (1 - p) values as a gene-level measure of differential expression.</p> <p>Results</p> <p>We applied the technique to the HGU-133A, HG-U95A, and "Golden Spike" spike-in data sets. The resulting receiver operating characteristic (ROC) curves compared favorably with other published results. This procedure is quite sensitive, so much so that it has revealed the presence of probe sets that might properly be called "unanticipated positives" rather than "false positives", because plots of these probe sets strongly suggest that they are differentially expressed.</p> <p>Conclusion</p> <p>The median ANOVA (1-p) approach presented here is a very simple methodology that does not depend on any specific probe level or probe models, and does not require any pre-processing other than within-chip standardization of probe level log amplitudes. Its performance is comparable to other published methods on the standard spike-in data sets, and has revealed the presence of new categories of probe sets that might properly be referred to as "unanticipated positives" and "unanticipated negatives" that need to be taken into account when using spiked-in data sets at "truthed" test beds.</p

Knockdown of MBP-1 in Human Foreskin Fibroblasts Induces p53-p21 Dependent Senescence

MBP-1 acts as a general transcriptional repressor. Overexpression of MBP-1 induces cell death in a number of cancer cells and regresses tumor growth. However, the function of endogenous MBP-1 in normal cell growth regulation remains unknown. To unravel the role of endogenous MBP-1, we knocked down MBP-1 expression in primary human foreskin fibroblasts (HFF) by RNA interference. Knockdown of MBP-1 in HFF (HFF-MBPsi-4) resulted in an induction of premature senescence, displayed flattened cell morphology, and increased senescence-associated beta-galactosidase activity. FACS analysis of HFF-MBPsi-4 revealed accumulation of a high number of cells in the G1-phase. A significant upregulation of cyclin D1 and reduction of cyclin A was detected in HFF-MBPsi-4 as compared to control HFF. Senescent fibroblasts exhibited enhanced expression of phosphorylated and acetylated p53, and cyclin-dependent kinase inhibitor, p21. Further analysis suggested that promyolocytic leukemia protein (PML) bodies are dramatically increased in HFF-MBPsi-4. Together, these results demonstrated that knockdown of endogenous MBP-1 is involved in cellular senescence of HFF through p53-p21 pathway

Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty

Background: Accurate estimation of statistical significance of a pairwise alignment is an important problem in sequence comparison. Recently, a comparative study of pairwise statistical significance with database statistical significance was conducted. In this paper, we extend the earlier work on pairwise statistical significance by incorporating with it the use of multiple parameter sets. Results: Results for a knowledge discovery application of homology detection reveal that using multiple parameter sets for pairwise statistical significance estimates gives better coverage than using a single parameter set, at least at some error levels. Further, the results of pairwise statistical significance using multiple parameter sets are shown to be significantly better than database statistical significance estimates reported by BLAST and PSI-BLAST, and comparable and at times significantly better than SSEARCH. Using non-zero parameter set change penalty values give better performance than zero penalty. Conclusion: The fact that the homology detection performance does not degrade when using multiple parameter sets is a strong evidence for the validity of the assumption that the alignment score distribution follows an extreme value distribution even when using multiple parameter sets. Parameter set change penalty is a useful parameter for alignment using multiple parameter sets. Pairwise statistical significance using multiple parameter sets can be effectively used to determine the relatedness of a (or a few) pair(s) of sequences without performing a time-consuming database search

SPH Simulations of Negative (Nodal) Superhumps: A Parametric Study

Negative superhumps in cataclysmic variable systems result when the accretion disc is tilted with respect to the orbital plane. The line of nodes of the tilted disc precesses slowly in the retrograde direction, resulting in a photometric signal with a period slightly less than the orbital period. We use the method of smoothed particle hydrodynamics to simulate a series of models of differing mass ratio and effective viscosity to determine the retrograde precession period and superhump period deficit $\varepsilon_-$ as a function of system mass ratio $q$. We tabulate our results and present fits to both $\varepsilon_-$ and $\varepsilon_+$ versus $q$, as well as compare the numerical results with those compiled from the literature of negative superhump observations. One surprising is that while we find negative superhumps most clearly in simulations with an accretion stream present, we also find evidence for negative superhumps in simulations in which we shut off the mass transfer stream completely, indicating that the origin of the photometric signal is more complicated than previously believed.Comment: 14 pages, 15 figures. Accepted for publication in MNRA

Imaging Oxygen Distribution in Marine Sediments. The Importance of Bioturbation and Sediment Heterogeneity

The influence of sediment oxygen heterogeneity, due to bioturbation, on diffusive oxygen flux was investigated. Laboratory experiments were carried out with 3 macrobenthic species presenting different bioturbation behaviour patterns:the polychaetes Nereis diversicolor and Nereis virens, both constructing ventilated galleries in the sediment column, and the gastropod Cyclope neritea, a burrowing species which does not build any structure. Oxygen two-dimensional distribution in sediments was quantified by means of the optical planar optode technique. Diffusive oxygen fluxes (mean and integrated) and a variability index were calculated on the captured oxygen images. All species increased sediment oxygen heterogeneity compared to the controls without animals. This was particularly noticeable with the polychaetes because of the construction of more or less complex burrows. Integrated diffusive oxygen flux increased with oxygen heterogeneity due to the production of interface available for solute exchanges between overlying water and sediments. This work shows that sediment heterogeneity is an important feature of the control of oxygen exchanges at the sediment–water interface

Fluoromycobacteriophages for rapid, specific, and sensitive antibiotic susceptibility testing of Mycobacterium tuberculosis

Rapid antibiotic susceptibility testing of Mycobacterium tuberculosis is of paramount importance as multiple- and extensively- drug resistant strains of M. tuberculosis emerge and spread. We describe here a virus-based assay in which fluoromycobacteriophages are used to deliver a GFP or ZsYellow fluorescent marker gene to M. tuberculosis, which can then be monitored by fluorescent detection approaches including fluorescent microscopy and flow cytometry. Pre-clinical evaluations show that addition of either Rifampicin or Streptomycin at the time of phage addition obliterates fluorescence in susceptible cells but not in isogenic resistant bacteria enabling drug sensitivity determination in less than 24 hours. Detection requires no substrate addition, fewer than 100 cells can be identified, and resistant bacteria can be detected within mixed populations. Fluorescence withstands fixation by paraformaldehyde providing enhanced biosafety for testing MDR-TB and XDR-TB infections. © 2009 Piuri et al

Uniform electron gases

We show that the traditional concept of the uniform electron gas (UEG) --- a homogeneous system of finite density, consisting of an infinite number of electrons in an infinite volume --- is inadequate to model the UEGs that arise in finite systems. We argue that, in general, a UEG is characterized by at least two parameters, \textit{viz.} the usual one-electron density parameter $\rho$ and a new two-electron parameter $\eta$. We outline a systematic strategy to determine a new density functional $E(\rho,\eta)$ across the spectrum of possible $\rho$ and $\eta$ values.Comment: 8 pages, 2 figures, 5 table