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

Bucillamine prevents cisplatin-induced ototoxicity through induction of glutathione and antioxidant genes.

Bucillamine is used for the treatment of rheumatoid arthritis. This study investigated the protective effects of bucillamine against cisplatin-induced damage in auditory cells, the organ of Corti from postnatal rats (P2) and adult Balb/C mice. Cisplatin increases the catalytic activity of caspase-3 and caspase-8 proteases and the production of free radicals, which were significantly suppressed by pretreatment with bucillamine. Bucillamine induces the intranuclear translocation of Nrf2 and thereby increases the expression of γ-glutamylcysteine synthetase (γ-GCS) and glutathione synthetase (GSS), which further induces intracellular antioxidant glutathione (GSH), heme oxygenase 1 (HO-1) and superoxide dismutase 2 (SOD2). However, knockdown studies of HO-1 and SOD2 suggest that the protective effect of bucillamine against cisplatin is independent of the enzymatic activity of HO-1 and SOD. Furthermore, pretreatment with bucillamine protects sensory hair cells on organ of Corti explants from cisplatin-induced cytotoxicity concomitantly with inhibition of caspase-3 activation. The auditory-brainstem-evoked response of cisplatin-injected mice shows marked increases in hearing threshold shifts, which was markedly suppressed by pretreatment with bucillamine in vivo. Taken together, bucillamine protects sensory hair cells from cisplatin through a scavenging effect on itself, as well as the induction of intracellular GSH

Recognition of adherent polychaetes on oysters and scallops using Microsoft Azure Custom Vision

Oyster and scallop cultures have high growth rates in the Korean aquaculture industry. However, their production is declining because of the manual selection of polychaete-adherent oysters and scallops. In this study, an artificial intelligence model for automatic selection of polychaetes was developed using Microsoft Azure Custom Vision to improve the productivity of oysters and scallops. A camera booth was built to capture images of oysters and scallops from various angles. Polychaetes in the images were tagged. Transfer learning available with Custom Vision was performed on the acquired images. By repeating the training and evaluation, the number of training images was increased by analyzing the precision, recall, and mean average precision using the Compact [S1] and General [A1] domains of Custom Vision. This paper presents the artificial intelligence model developed for the automatic selection of polychaete-adherent oysters and scallops as well as the optimal model development method using Microsoft Azure Custom Vision

Low Level Light Could Work on Skin Inflammatory Disease: A Case Report on Refractory Acrodermatitis Continua

Low level laser or light treatment on the various clinical condition is getting considerable attention now. However, there has been no report about the clinical effect of low level polarized polychromatic noncoherent light (LPPL) on the inflammatory skin disease. We experienced a case of acrodermatitis continua in a pregnant woman refractory to any conventional treatment including the most potent topical steroid. She was successfully treated with LPPL. LPPL could be a possible treatment modality producing substantial clinical result in inflammatory skin condition without any side-effect

Clinical significance of amyloid β positivity in patients with probable cerebral amyloid angiopathy markers

Purpose: We investigated the frequency and clinical significance of amyloid β (Aβ) positivity on PET in patients with cerebral amyloid angiopathy (CAA). / Methods: We recruited 65 patients who met the modified Boston criteria for probable CAA. All underwent amyloid PET, MRI, APOE genotyping and neuropsychological testing, and we obtained information on MRI markers of CAA and ischemic cerebral small-vessel disease (CSVD). We investigated the CAA/ischemic CSVD burden and APOE genotypes in relation to Aβ positivity and investigated the effect of Aβ positivity on longitudinal cognitive decline. / Results: Among the 65 CAA patients, 43 (66.2%) showed Aβ PET positivity (Aβ+). Patients with Aβ+ CAA had more lobar microbleeds (median 9, interquartile range 2–41, vs. 3, 2–8; P = 0.045) and a higher frequency of cortical superficial siderosis (34.9% vs. 9.1%; P = 0.025), while patients with Aβ− CAA had more lacunes (1, 0–2, vs. 0, 0–1; P = 0.029) and a higher frequency of severe white matter hyperintensities (45.5% vs. 20.9%; P = 0.040). The frequency of ε4 carriers was higher in Aβ+ patients (57.1%) than in Aβ− patients (18.2%; P = 0.003), while the frequency of ε2 carriers did not differ between the two groups. Finally, Aβ positivity was associated with faster decline in multiple cognitive domains including language (P < 0.001), visuospatial function (P < 0.001), and verbal memory (P < 0.001) in linear mixed effects models. / Conclusion: Our findings suggest that a significant proportion of patients with probable CAA in a memory clinic are Aβ− on PET. Aβ positivity in CAA patients is associated with a distinct pattern of CSVD biomarker expression, and a worse cognitive trajectory. Aβ positivity has clinical relevance in CAA and might represent either advanced CAA or additional Alzheimer’s disease neuropathological changes

A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates

BACKGROUND: Studies of differential expression that use Affymetrix GeneChip arrays are often carried out with a limited number of replicates. Reasons for this include financial considerations and limits on the available amount of RNA for sample preparation. In addition, failed hybridizations are not uncommon leading to a further reduction in the number of replicates available for analysis. Most existing methods for studying differential expression rely on the availability of replicates and the demand for alternative methods that require few or no replicates is high. RESULTS: We describe a statistical procedure for performing differential expression analysis without replicates. The procedure relies on a Bayesian integrated approach (BGX) to the analysis of Affymetrix GeneChips. The BGX method estimates a posterior distribution of expression for each gene and condition, from a simultaneous consideration of the available probe intensities representing the gene in a condition. Importantly, posterior distributions of expression are obtained regardless of the number of replicates available. We exploit these posterior distributions to create ranked gene lists that take into account the estimated expression difference as well as its associated uncertainty. We estimate the proportion of non-differentially expressed genes empirically, allowing an informed choice of cut-off for the ranked gene list, adapting an approach proposed by Efron. We assess the performance of the method, and compare it to those of other methods, on publicly available spike-in data sets, as well as in a proper biological setting. CONCLUSION: The method presented is a powerful tool for extracting information on differential expression from GeneChip expression studies with limited or no replicates