Comparison of sequence-dependent tiling array normalization approaches

<p>Abstract</p> <p>Background</p> <p>The detection of enriched DNA or RNA fragments by tiling microarrays has become more and more popular. These microarrays contain a high number of small probes covering genomic loci. However, to achieve high coverage the probe sequences cannot be selected for their hybridization properties. The affinity of the probes towards their targets varies in a sequence-dependent manner. In order to remove this bias a number of approaches have been developed and shown to increase the detection of enriched DNA or RNA fragments. However, these approaches also employ a peak detection algorithm that is different from the one used previously. Thus, it seems possible that the enhancement of detection is due to the peak detection algorithm rather than the sequence-dependent normalization.</p> <p>Results</p> <p>We compared three different sequence-dependent probe level normalization procedures to a naïve sequence-independent normalization technique. In order to achieve maximal comparability, we used the normalized intensity values as input to a single peak detection algorithm. A so-called "spike-in" data set served as benchmark for the performance. We will show that the sequence-dependent normalization procedures do not perform better than the naïve approach, suggesting that the benefit of using these normalization approaches is limited. Furthermore, we will show that the naïve approach does well, because it effectively removes the sequence-dependent component of the measured intensities with the help of the control hybridization experiment.</p> <p>Conclusion</p> <p>Sequence-dependent normalization of microarray data hardly improves the detection of enriched DNA or RNA fragments. The "success" of the sequence-independent naïve approach is only possible due to the control experiment and requires proper scaling of the measured intensities.</p

Total Empiricism: Learning from Data

Statistical analysis is an important tool to distinguish systematic from chance findings. Current statistical analyses rely on distributional assumptions reflecting the structure of some underlying model, which if not met lead to problems in the analysis and interpretation of the results. Instead of trying to fix the model or "correct" the data, we here describe a totally empirical statistical approach that does not rely on ad hoc distributional assumptions in order to overcome many problems in contemporary statistics. Starting from elementary combinatorics, we motivate an information-guided formalism to quantify knowledge extracted from the given data. Subsequently, we derive model-agnostic methods to identify patterns that are solely evidenced by the data based on our prior knowledge. The data-centric character of empiricism allows for its universal applicability, particularly as sample size grows larger. In this comprehensive framework, we re-interpret and extend model distributions, scores and statistical tests used in different schools of statistics.Comment: Keywords: effective description, large-N, operator formalism, statistical testing, inference, information divergenc

Eliminating confounder-induced bias in the statistics of intervention

Experimental and observational studies often lead to spurious association between the outcome and independent variables describing the intervention, because of confounding to third-party factors. Even in randomized clinical trials, confounding might be unavoidable due to small sample sizes. Practically, this poses a problem, because it is either expensive to re-design and conduct a new study or even impossible to alleviate the contribution of some confounders due to e.g. ethical concerns. Here, we propose a method to consistently derive hypothetical studies that retain as many of the dependencies in the original study as mathematically possible, while removing any association of observed confounders to the independent variables. Using historic studies, we illustrate how the confounding-free scenario re-estimates the effect size of the intervention. The new effect size estimate represents a concise prediction in the hypothetical scenario which paves a way from the original data towards the design of future studies.Comment: 16 pages, 5 figures, 3 table

On the estimation and interpretation of effect size metrics

Effect size estimates are thought to capture the collective, two-way response to an intervention or exposure in a three-way problem among the intervention/exposure, various confounders and the outcome. For meaningful causal inference from the estimated effect size, the joint distribution of observed confounders must be identical across all intervention/exposure groups. However, real-world observational studies and even randomized clinical trials often lack such structural symmetry. To address this issue, various methods have been proposed and widely utilized. Recently, elementary combinatorics and information theory have motivated a consistent way to completely eliminate observed confounding in any given study. In this work, we leverage these new techniques to evaluate conventional methods based on their ability to (a) consistently differentiate between collective and individual responses to intervention/exposure and (b) establish the desired structural parity for sensible effect size estimation. Our findings reveal that a straightforward application of logistic regression homogenizes the three-way stratified analysis, but fails to restore structural symmetry leaving in particular the two-way effect size estimate unadjusted. Conversely, the Mantel-Haenszel estimator struggles to separate three-way effects from the two-way effect of intervention/exposure, leading to inconsistencies in interpreting pooled estimates as two-way risk metrics.Comment: 10 pages, 1 Figure, 3 diagrams, 2 table

The Zinc Finger Associated Domain of Drosophila melanogaster, its Evolution and Phylogenetic Restriction

The Drosophila melanogaster genome contains 359 C2H2 zinc finger protein (ZFP) coding genes. During an in-depth analysis of these proteins I identified a sequence motif that can be found at the N-terminus of 94 ZFP coding genes (26.1%). It has been named zinc finger associated domain (ZAD), since it is almost exclusively asociated with C2H2 zinc finger motifs, with the exception of four genes that code for proteins with isolated ZADs. The ZAD represents an independently folding domain that is stabilised by zinc coordination. It mediates homodimer formation and probably association of closely related ZAD family members. The ZAD coding genes fall into two large subsets: subset 1 where the ZAD is encoded by a single exon and subset 2 where the ZAD is coded by two exons. I propose that subset 1 ZADs have lost their intron at multiple time points by distinct retroposition events. The majority of ZAD coding genes in Drosophila melanogaster were generated by local gene duplication events, which is consistent with the observation that the ZAD coding genes participates in lineage-specific expansions in three fly species. The finding that many ZAD coding genes are specific for a given species prompted the idea that these genes may be involved in mechanisms that maintain genetic divergence during speciation. My results show that ZAD coding genes are overrepresented in a class of genes that represent putative "speciation genes".Das Drosophila melanogaster Genom enthält 359 C2H2 Zink Finger Protein (ZFP) kodierende Gene. Während der Analyse dieser Proteine konnte ich ein Sequenzmotiv identifizieren, welches am N-Terminus von 94 ZFP kodierenden Genen (26,1%) auftritt. Es wurde Zink Finger assoziierte Domäne genannt, da es fast auschließlich mit C2H2 Zink Finger Motiven assoziiert ist und nur bei vier Genen auftritt, die Proteine mit isolierten ZADs kodieren. Die ZAD ist eine unabhängig faltende Domäne, die durch Zink Koordination stabilisiert wird. Sie ermöglicht die Bildung von Homodimeren und wahrscheinlich die Bindung zwischen nah verwandten ZADs. Die ZADs kann man in zwei Klassen einteilen: Klasse 1, bei welchen die ZAD durch ein Exon kodiert wird, und Klasse 2, welche durch zwei Exons kodiert werden. Die ZADs der Klasse 1 haben ihr Intron wahrscheinlich mehrfach und unabhängig durch Retropositionsereignisse verloren. Die meisten ZAD kodierenden Gene von Drosophila melanogaster wurden durch lokale Genduplikationen erzeugt, was mit der Beobachtung übereinstimmt, dass die ZAD an "lineage-specific expansions" in drei Fliegenarten teilnimmt. Die Beobachtung, dass viele ZAD kodierende Gene spezifisch für eine gegebene Art sind, führte zu der Idee, dass diese an Mechanismen beteiligt sind, die die genetische Divergenz während des Artbildungsprozesses aufrecht erhalten. Meine Ergebnisse zeigen, dass ZAD kodierende Gene überproportional häufig in einer Klasse von möglichen "Speziationsgenen" vorkommen

The biological significance of non-enzymatic reaction of menadione with plasma thiols: enhancement of menadione-induced cytotoxicity to platelets by the presence of blood plasma

AbstractTo test the hypothesis that the non-enzymatic reaction of quinones with thiols in plasma can generate reactive oxygens (ROS), thereby leading to potentiated cellular toxicity, we have studied the effect of a representative quinone compound, menadione, on plasma isolated from rats. The experimental results are as follows: (1) menadione generated ROS via non-enzymatic reaction with protein thiols in plasma; (2) the presence of plasma increased menadione-induced cytotoxicity to platelets; (3) pretreatment of plasma with a thiol-depleting agent significantly suppressed menadione-induced ROS and cytotoxicity. These results suggest that the non-enzymatic reaction of menadione with plasma thiols could be an important process in quinone-induced cellular toxicity

reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T cells

The combinatorial action of co-localizing chromatin modifications and regulators determines chromatin structure and function. However, identifying co-localizing chromatin features in a high-throughput manner remains a technical challenge. Here we describe a novel reChIP-seq approach and tailored bioinformatic analysis tool, normR that allows for the sequential enrichment and detection of co-localizing DNA-associated proteins in an unbiased and genome-wide manner. We illustrate the utility of the reChIP-seq method and normR by identifying H3K4me3 or H3K27me3 bivalently modified nucleosomes in primary human CD4+ memory T cells. We unravel widespread bivalency at hypomethylated CpG-islands coinciding with inactive promoters of developmental regulators. reChIP-seq additionally uncovered heterogeneous bivalency in the population, which was undetectable by intersecting H3K4me3 and H3K27me3 ChIP- seq tracks. Finally, we provide evidence that bivalency is established and stabilized by an interplay between the genome and epigenome. Our reChIP-seq approach augments conventional ChIP-seq and is broadly applicable to unravel combinatorial modes of action

Prevention of mitochondrial impairment by inhibition of protein phosphatase 1 activity in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease caused by progressive loss of motor neurons (MNs) and subsequent muscle weakness. These pathological features are associated with numerous cellular changes, including alteration in mitochondrial morphology and function. However, the molecular mechanisms associating mitochondrial structure with ALS pathology are poorly understood. In this study, we found that Dynamin-related protein 1 (Drp1) was dephosphorylated in several ALS models, including those with SOD1 and TDP-43 mutations, and the dephosphorylation was mediated by the pathological induction of protein phosphatase 1 (PP1) activity in these models. Suppression of the PP1-Drp1 cascade effectively prevented ALS-related symptoms, including mitochondrial fragmentation, mitochondrial complex I impairment, axonal degeneration, and cell death, in primary neuronal culture models, iPSC-derived human MNs, and zebrafish models in vivo. These results suggest that modulation of PP1-Drp1 activity may be a therapeutic target for multiple pathological features of ALS

Genetic Study in a Case of Birt-Hogg-Dubé Syndrome

Birt-Hogg-Dubé syndrome (BHDS) is an autosomal dominantly inherited disorder characterized by multiple trichodiscomas, fibrofolliculomas, and acrocordons. There is also an increased risk of developing renal neoplasms and lung cysts/spontaneous pneumothorax. We present a 43-year-old man with multiple, 2~4 mm sized, dome-shaped, and skin-colored papules on his cheek and neck. On the basis of clinical finding and histopathologic examination on the cheek lesion, it was diagnosed as multiple trichodiscomas. Subsequently, molecular analysis revealed a mutation in the folliculin gene. We report a rare case of BHDS with a proved gene mutation