Practical Data Analysis for Designed Experiments

Yandell, Brian S.

doi:10.1007/978-1-4899-3035-4

Cited by 255 publications

(186 citation statements)

References 0 publications

Supporting

Mentioning

181

Contrasting

Unclassified

Order By: Relevance

“…http://dx.doi.org/10.1101/209676 doi: bioRxiv preprint first posted online We first discretized the time series phosphoproteomic data, using Tukey's Honest Significant Difference (HSD) test (Yandell, 1997) to determine whether a peptide exhibits a significant increase, significant decrease, or no change in phosphorylation at each post-stimulation time point. Significant phosphorylation changes can be relative to either the pre-stimulation baseline level or the previous time point.…”

Section: Reconstructing the Egfr Pathway With Tps Explains Temporal Pmentioning

confidence: 99%

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

Köksal

Beck

Cronin

et al. 2017

Preprint

View full text Add to dashboard Cite

Advances in proteomics reveal that pathway databases fail to capture the majority of cellular signaling activity. Our mass spectrometry study of the dynamic epidermal growth factor (EGF) response demonstrates that over 89% of significantly (de)phosphorylated proteins are excluded from individual EGF signaling maps, and 63% are absent from all annotated pathways. We present a computational method, the Temporal Pathway Synthesizer (TPS), to discover missing pathway elements by modeling temporal phosphoproteomic data. TPS uses constraint solving to exhaustively explore all possible structures for a signaling pathway, eliminating structures that are inconsistent with protein-protein interactions or the observed phosphorylation event timing. Applied to our EGF response data, TPS connects 83% of the responding proteins to receptors and signaling proteins in EGF pathway maps. Inhibiting predicted active kinases supports the TPS pathway model. The TPS algorithm is broadly applicable and also recovers an accurate model of the yeast osmotic stress response.

show abstract

Section: Reconstructing the Egfr Pathway With Tps Explains Temporal Pmentioning

confidence: 99%

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

Köksal

Beck

Cronin

et al. 2017

Preprint

View full text Add to dashboard Cite

show abstract

“…Future work will allow for spatial priors and for priors allowing information to be aggregated over voxels and subjects. For example, for a random effects analysis [36] of data from multiple subjects a hierarchical prior such as p(w|α) = N(w pop , α −1 I)…”

Section: Priorsmentioning

confidence: 99%

Variational Bayesian inference for fMRI time series

Penny¹,

Kiebel²,

Friston³

2003

NeuroImage

193

166

View full text Add to dashboard Cite

We describe a Bayesian estimation and inference procedure for fMRI time series based on the use of General Linear Models with Autoregressive (AR) error processes. We make use of the Variational Bayesian (VB) framework which approximates the true posterior density with a factorised density. The fidelity of this approximation is verified via Gibbs sampling. The VB approach provides a natural extension to previous Bayesian analyses which have used Empirical Bayes. VB has the advantage of taking into account the variability of hyperparameter estimates with little additional computational effort. Further, VB allows for automatic selection of the order of the AR process. Results are shown on simulated data and on data from an event-related fMRI experiment.

show abstract

“…All transformations, filtering, normalization, and statistical analyses were performed with software developed by the Interdisciplinary Center for Biotechnology Research. The statistical package, R, serves as the backend for ANOVA and Tukey's HSD (20) in this software.…”

Section: Real-time Quantitative Pcr (Q-pcr)mentioning

confidence: 99%

A global view of the selectivity of zinc deprivation and excess on genes expressed in human THP-1 mononuclear cells

Cousins

Blanchard

Popp

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

168

133

View full text Add to dashboard Cite

Among the micronutrients required by humans, zinc has particularly divergent modes of action. cDNA microarray and quantitative PCR technologies were used to investigate the zinc responsiveness of known genes that influence zinc homeostasis and to identify, through global screening, genes that may relate to phenotypic outcomes of altered dietary zinc intake. Human monocytic͞ macrophage THP-1 cells were either acutely zinc depleted, using a cell-permeable zinc-specific chelator, or were supplemented with zinc to alter intracellular zinc concentrations. Initially, genes associated with zinc homeostasis were evaluated by quantitative PCR to establish ranges for fold changes in transcript abundance that might be expected with global screening. Zinc transporter-1 and zinc transporter-7 expression increased when cellular zinc increased, whereas Zip-2 expression, the most zinc-responsive gene examined, was markedly increased by zinc depletion. Microarrays composed of Ϸ22,000 elements were used to identify those genes responsive to either zinc depletion, zinc supplementation, or both conditions. Hierarchal clustering and ANOVA revealed that Ϸ5% or 1,045 genes were zinc responsive. Further sorting based on this pattern of the zinc responsiveness of these genes into seven groups revealed that 104 genes were linearly zinc responsive in a positive mode (i.e., increased expression as cellular zinc increases) and 86 genes that were linearly zinc responsive in a negative mode (i.e., decreased expression as cellular zinc increases). Expression of some genes was responsive to only zinc depletion or supplementation. Categorization by function revealed numerous genes needed for host defense were among those identified as zinc responsive, including cytokine receptors and genes associated with amplification of the Th1 immune response.nutrition ͉ genomics ͉ functional genomics ͉ immunology ͉ microarray

show abstract

Practical Data Analysis for Designed Experiments

Cited by 255 publications

References 0 publications

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

Variational Bayesian inference for fMRI time series

A global view of the selectivity of zinc deprivation and excess on genes expressed in human THP-1 mononuclear cells

Contact Info

Product

Resources

About