Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples

BACKGROUND: Gene expression microarray technology continues to evolve and its use has expanded into all areas of biology. However, the high dimensionality of the data makes analysis a difficult challenge. Evaluating measurements and estimating the significance of the observed differences among samples remain important issues that must be addressed for each technology platform. In this work we use a consecutive sampling method to characterize the dispersion patterns of data generated from Illumina fiberoptic bead-based oligonucleotide arrays. RESULTS: To describe general properties of the dispersion we used a linear function SD = a + bY(mean), approximating the standard deviation across arrays (Y(mean )is the mean expression of a given consecutive sample). First we examined three levels of variability: 1) same cell culture, same reverse transcription, duplicate hybridizations; 2) same cell culture, reverse transcription replicates; 3) parallel cultures. Each higher level is expected to introduce a new source of variability. We observed minor differences in the constant term: the mean values are 3.5, 3.1 and 3.5, respectively. However, the mean coefficient b increased from 0.045 to 0.147 and 0.133. We compared the coefficients derived from the consecutive sampling to those obtained from the standard deviation of individual gene expressions and found them in good agreement. In the second experiment samples we detected 11 genes with systematically different expressions between the experiment samples treated with glucose oxidase and controls and corroborated the selection using the Mann-Whitney and other tests. We also compared the consecutive sampling and coincidence method to t-test: the average percentage of consistency was above 80 for the former and below 50 for the latter. CONCLUSION: Our results indicate that the consecutive sampling method and standard deviation function provide a convenient description of the overall dispersion of Illumina arrays. We observed that the constant term of the standard deviation function is at average approximately the same for duplicate hybridization as for the assays with additional sources of variability. Furthermore, among the genes affected by glucose oxidase treatment we identified 6 genes in oxidative stress pathways and 5 genes involved in DNA repair. Finally, we noted that the consecutive sampling and coincidence test provide, under given conditions, more consistent results than the t-test. REVIEWERS: This article was reviewed by Alexander Karpikov (nominated by MarkGerstein), Jordan King and Eugene V. Koonin

Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution

BACKGROUND: DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inherent variability of DNA microarray data, many new statistical methods have been developed for evaluating the significance of the observed differences in gene expression. However, until now little attention has been given to the characterization of dispersion of DNA microarray data. RESULTS: Here we examine the expression data obtained from 682 Affymetrix GeneChips(® )with 22 different types and we demonstrate that the Gaussian (normal) frequency distribution is characteristic for the variability of gene expression values. However, typically 5 to 15% of the samples deviate from normality. Furthermore, it is shown that the frequency distributions of the difference of expression in subsets of ordered, consecutive pairs of genes (consecutive samples) in pair-wise comparisons of replicate experiments are also normal. We describe a consecutive sampling method, which is employed to calculate the characteristic function approximating standard deviation and show that the standard deviation derived from the consecutive samples is equivalent to the standard deviation obtained from individual genes. Finally, we determine the boundaries of probability intervals and demonstrate that the coefficients defining the intervals are independent of sample characteristics, variability of data, laboratory conditions and type of chips. These coefficients are very closely correlated with Student's t-distribution. CONCLUSION: In this study we ascertained that the non-systematic variations possess Gaussian distribution, determined the probability intervals and demonstrated that the K(α )coefficients defining these intervals are invariant; these coefficients offer a convenient universal measure of dispersion of data. The fact that the K(α )distributions are so close to t-distribution and independent of conditions and type of arrays suggests that the quantitative data provided by Affymetrix technology give "true" representation of physical processes, involved in measurement of RNA abundance. REVIEWERS: This article was reviewed by Yoav Gilad (nominated by Doron Lancet), Sach Mukherjee (nominated by Sandrine Dudoit) and Amir Niknejad and Shmuel Friedland (nominated by Neil Smalheiser)

Band structure of CuMnAs probed by optical and photoemission spectroscopy

5 pages, 5 figures + Supplementary InformationTetragonal phase of CuMnAs progressively appears as one of the key materials for antiferromagnetic spintronics due to efficient current-induced spin-orbit torques whose existence can be directly inferred from crystal symmetry. Theoretical understanding of spintronic phenomena in this material, however, relies on the detailed knowledge of electronic structure (band structure and corresponding wave functions) which has so far been tested only to a limited extent. We show that AC permittivity (obtained from ellipsometry) and UV photoelectron spectra agree with density functional calculations. Together with the x-ray diffraction and precession electron diffraction tomography, our analysis confirms recent theoretical claim [Phys.Rev.B 96, 094406 (2017)] that copper atoms occupy lattice positions in the basal plane of the tetragonal unit cell.We acknowledge support from National Grid Infrastructure MetaCentrum provided under the programme “Projects of Large Research, Development, and Innovations Infrastructures” (CESNET LM2015042); Grant Agency of the Czech Republic under Grant No. 15-13436S; CEDAMNF (CZ.02.1.01/0.0/0.0/15_003/0000358) of the Czech ministry of education (MŠMT) as well as its LM2015087 and LNSMLNSpin grants; Cariplo Foundation, Grant No. 2013-0726 (MAGISTER); Spanish MINECO under MAT2015-67593-P project and the ‘Severo Ochoa’ Programme (SEV-2015-0496); EU FET Open RIA Grant No. 766566; Engineering and Physical Sciences Research Council Grant No. EP/P019749/1. P.W. acknowledges support from the Royal Society through a University Research Fellowship.Peer reviewe

Abstracts from the 20th International Symposium on Signal Transduction at the Blood-Brain Barriers

https://deepblue.lib.umich.edu/bitstream/2027.42/138963/1/12987_2017_Article_71.pd