proDA: Probabilistic Dropout Analysis for Identifying Differentially Abundant Proteins in Label-Free Mass Spectrometry

Ahlmann-Eltze, Constantin; Anders, Simon

doi:10.1101/661496

Cited by 38 publications

(54 citation statements)

References 45 publications

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“…This method aims to combine the sigmoidal dropout curve for missing values with the information from the observed values without direct value imputation. This allows for a more robust analysis that combines both the information from measured and missing values [ 22 ].…”

Section: Resultsmentioning

confidence: 99%

The Human 2-Cys Peroxiredoxins form Widespread, Cysteine-Dependent- and Isoform-Specific Protein-Protein Interactions

et al. 2021

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Redox signaling is controlled by the reversible oxidation of cysteine thiols, a post-translational modification triggered by H2O2 acting as a second messenger. However, H2O2 actually reacts poorly with most cysteine thiols and it is not clear how H2O2 discriminates between cysteines to trigger appropriate signaling cascades in the presence of dedicated H2O2 scavengers like peroxiredoxins (PRDXs). It was recently suggested that peroxiredoxins act as peroxidases and facilitate H2O2-dependent oxidation of redox-regulated proteins via disulfide exchange reactions. It is unknown how the peroxiredoxin-based relay model achieves the selective substrate targeting required for adequate cellular signaling. Using a systematic mass-spectrometry-based approach to identify cysteine-dependent interactors of the five human 2-Cys peroxiredoxins, we show that all five human 2-Cys peroxiredoxins can form disulfide-dependent heterodimers with a large set of proteins. Each isoform displays a preference for a subset of disulfide-dependent binding partners, and we explore isoform-specific properties that might underlie this preference. We provide evidence that peroxiredoxin-based redox relays can proceed via two distinct molecular mechanisms. Altogether, our results support the theory that peroxiredoxins could play a role in providing not only reactivity but also selectivity in the transduction of peroxide signals to generate complex cellular signaling responses.

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Section: Resultsmentioning

confidence: 99%

The Human 2-Cys Peroxiredoxins form Widespread, Cysteine-Dependent- and Isoform-Specific Protein-Protein Interactions

et al. 2021

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“…Hypotheses, measures, and our analytical plan were pre-registered with the Open Science Framework: https://osf.io/rfndu/. All statistical analyses were performed in R studio (R Core Team, 2008), including the following packages: apaTables (Stanley, 2017), dplyr (Wickham, 2016), ggplot2 (Wickham, 2009), lemon (Edwards, 2017), ggsignif (Ahlmann-Eltze, 2017), psych (Revelle, 2015), reshape2 (Wickham, 2007), and Rmisc (Hope, 2013). The R script used for all data processing and analyses is available as an Electronic Supplement to this article, as is the dataset and an information sheet about the included variables.…”

Section: Methodsmentioning

confidence: 99%

Cuing both positive and negative episodic foresight reduces delay discounting but does not affect risk-taking

Bulley

Miloyan

Pepper

et al. 2019

Quarterly Journal of Experimental Psychology

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Humans frequently create mental models of the future, allowing outcomes to be inferred in advance of their occurrence. Recent evidence suggests that imagining positive future events reduces delay discounting (the devaluation of reward with time until its receipt), while imagining negative future events may increase it. Here, using a sample of 297 participants, we experimentally assess the effects of cued episodic simulation of positive and negative future scenarios on decision-making in the context of both delay discounting (monetary choice questionnaire) and risk-taking (balloon-analogue risk task). Participants discounted the future less when cued to imagine positive and negative future scenarios than they did when cued to engage in control neutral imagery. There were no effects of experimental condition on risk-taking. Thus, although these results replicate previous findings suggesting episodic future simulation can reduce delay discounting, they indicate that this effect is not dependent on the valence of the thoughts, and does not generalise to all other forms of “impulsive” decision-making. We discuss various interpretations of these results, and suggest avenues for further research on the role of prospection in decision-making.

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“…The statistical tests were performed on R Studio using “PMCMRPlus” ( Kessler et al, 2020 ) and “FSA” (Derek H. Ogle et al, 2021 ) packages. Data were plotted using R Studio “ggplot2” ( Hadley, 2016 ) and “ggsignif” ( Ahlmann-Eltze, 2019 ) packages. Cells with gene expression level < 0.2 were exclude from the violin plots and statistical analyses.…”

Section: Methodsmentioning

confidence: 99%

Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development

Zhang

Mandric

Nguyen

et al. 2021

Front. Cell Dev. Biol.

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The developing retina expresses multiple bHLH transcription factors. Their precise functions and interactions in uncommitted retinal progenitors remain to be fully elucidated. Here, we investigate the roles of bHLH factors ATOH7 and Neurog2 in human ES cell-derived retinal organoids. Single cell transcriptome analyses identify three states of proliferating retinal progenitors: pre-neurogenic, neurogenic, and cell cycle-exiting progenitors. Each shows different expression profile of bHLH factors. The cell cycle-exiting progenitors feed into a postmitotic heterozygous neuroblast pool that gives rise to early born neuronal lineages. Elevating ATOH7 or Neurog2 expression accelerates the transition from the pre-neurogenic to the neurogenic state, and expands the exiting progenitor and neuroblast populations. In addition, ATOH7 and Neurog2 significantly, yet differentially, enhance retinal ganglion cell and cone photoreceptor production. Moreover, single cell transcriptome analyses reveal that ATOH7 and Neurog2 each assert positive autoregulation, and both suppress key bHLH factors associated with the pre-neurogenic and states and elevate bHLH factors expressed by exiting progenitors and differentiating neuroblasts. This study thus provides novel insight regarding how ATOH7 and Neurog2 impact human retinal progenitor behaviors and neuroblast fate choices.

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proDA: Probabilistic Dropout Analysis for Identifying Differentially Abundant Proteins in Label-Free Mass Spectrometry

Cited by 38 publications

References 45 publications

The Human 2-Cys Peroxiredoxins form Widespread, Cysteine-Dependent- and Isoform-Specific Protein-Protein Interactions

The Human 2-Cys Peroxiredoxins form Widespread, Cysteine-Dependent- and Isoform-Specific Protein-Protein Interactions

Cuing both positive and negative episodic foresight reduces delay discounting but does not affect risk-taking

Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development

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