Retroviral Guide

Consensus Clustering And Functional Interpretation Of Gene-expression Data
Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NF?B and the unfolded protein response in certain B-cell lymphomas.... More

[review] From Fluctuations To Phenotypes: The Physiology Of Noise
In both single-celled organisms and multicellular organisms, stochastic changes in gene expression lead to different cellular fates... More

3d Morphology And Gene Expression In Thedrosophila Blastoderm At Cellular Resolution Ii: Dynamics
Background: To accurately describe gene expression and computationally model animal transcriptional networks, it is essential to determine the changing locations of cells in developing embryos. Results: Using automated image analysis methods, we provide the first quantitative description of temporal changes in morphology and gene expression with cellular resolution in whole embryos, using the Drosophila blastoderm as a model. Analyses based on both fixed and live embryos reveal complex, previously undetected three-dimensional changes in nuclear density patterns caused by nuclear movements prior to gastrulation. Gene expression patterns move in part with these changes in morphology, but additional spatial shifts in expression patterns are also seen, supporting a previously proposed model of pattern dynamics based on the induction and inhibition of gene expression. We show that mutations that disrupt either the anterior/posterior (a/p) or the dorsal/ventral (d/v) transcriptional cascades alter morphology and gene expression along both the a/p and d/v axes in a way suggesting that these two patterning systems interact via both transcriptional and morphological mechanisms. Conclusions: Our work establishes a new strategy for measuring temporal changes in the locations of cells and gene expression patterns that uses fixed cell material and computational modeling. It also provides a coordinate framework for the blastoderm embryo that will allow increasingly accurate spatio-temporal modeling of both the transcriptional control network and morphogenesis.... More

Clustering Of Genes Into Regulons Using Integrated Modeling-cogrim
We present a Bayesian hierarchical model and Gibbs Sampling implementation that integrates gene expression, ChIP binding and transcription factor motif data in a principled and robust fashion. COGRIM was applied to both unicellular and mammalian organisms under different scenarios of available data. In these applications, we demonstrate the ability to predict gene-transcription factor interactions with reduced levels of false positives as well as make predictions beyond what is obtained considering single types of data... More

Filamins Tether Cftr To The Cell Surface
Cystic fibrosis (CF) is caused by mutations in a gene that encodes a protein known as CFTR. More than 1000 different disease-causing mutations in CFTR have been identified, and although the overall effect of each mutation is to decrease CFTR expression at the cell surface, it is not known for every one of these mutations what the molecular defect is that causes the decreased cell surface expression of CFTR. [click link for full article]... More

MPAM EzyFeeds

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