Oligonucleotide arrays can provide a broad picture of the state cell, by monitoring expression level thousands genes at same time. It is interest to develop techniques for extracting useful information from resulting data sets. Here we report application two-way clustering method analyzing set consisting patterns different cell types. Gene in 40 tumor and 22 normal colon tissue samples was analyzed with an Affymetrix oligonucleotide array complementary more than 6,500 human genes. An...

A wide range of organisms use circadian clocks to keep internal sense daily time and regulate their behavior accordingly. Most these intracellular genetic networks based on positive negative regulatory elements. The integration “circuits” at the cellular level imposes strong constraints functioning design. Here, we study a recently proposed model [Barkai, N. & Leibler, S. (2000) Nature (London) , 403, 267–268] that incorporates just essential elements found experimentally. We show this...

We present an approach for the analysis of genome-wide expression data. Our method is designed to overcome limitations traditional techniques, when applied large-scale Rather than alloting each gene a single cluster, we assign both genes and conditions context-dependent potentially overlapping transcription modules. provide rigorous definition module as object be retrieved from An efficient algorithm, which searches modules encoded in data by iteratively refining sets until they match this...

During evolution, novel phenotypes emerge through changes in gene expression, but the genetic basis is poorly understood. We compared allele-specific expression of two yeast species and their hybrid, which allowed us to distinguish regulatory sequences itself (cis) from upstream factors (trans). Expression divergence between was generally due cis. Divergence trans reflected a differential response environment explained tendency certain genes diverge rapidly. Hybrid-specific deviating...

Chromatin structure is central for the regulation of gene expression, but its genome-wide organization only beginning to be understood. Here, we examine connection between patterns nucleosome occupancy and capacity modulate expression upon changing conditions, i.e., transcriptional plasticity. By analyzing data positioning in yeast, find that presence nucleosomes close transcription start site associated with high plasticity, while at more distant upstream positions are negatively correlated...

The economy of protein production is central to cell physiology, being intimately linked with division rate and size. Attempts model cellular physiology are limited by the scarcity experimental data defining molecular processes limiting expression. Here, we distinguish relative contribution gene transcription translation slower proliferation budding yeast producing excess levels unneeded proteins. In contrast widely held assumptions, rapidly growing cells not universally ribosome content....

Growing cells coordinate protein translation with metabolic rates. Central to this coordination is ribosome production. Ribosomes drive cell growth, but of ribosomal proteins competes production non-ribosomal proteins. Theory shows that growth maximized when all expressed ribosomes are constantly translating. To examine whether budding yeast function at limit full usage, we profiled the proteomes growing in different environments. We find produce excess proteins, amounting a constant ≈8%...

Comparing genomic properties of different organisms is fundamental importance in the study biological and evolutionary principles. Although differences among are often attributed to differential gene expression, genome-wide comparative analysis thus far has been based primarily on sequence information. We present a large datasets expression profiles from six evolutionarily distant organisms: S. cerevisiae, C. elegans, E. coli, A. thaliana, D. melanogaster, H. sapiens. use information connect...

Abstract Motivation: Large-scale gene expression data comprising a variety of cellular conditions hold the promise global view on transcription program. While conventional clustering algorithms have been successfully applied to smaller datasets, utility many for analysis large-scale is limited by their inability capture combinatorial and condition-specific co-regulation. In addition, there an increasing need integrate rapidly accumulating body other high-throughput biological with analysis....

Recent experiments revealed large-scale differences in the transcription programs of related species, yet little is known about genetic basis underlying evolution gene expression and its contribution to phenotypic diversity. Here we describe a modulation yeast program that connected emergence capacity for rapid anaerobic growth. Genes coding mitochondrial cytoplasmic ribosomal proteins display strongly correlated pattern Candida albicans, but this correlation lost fermentative Saccharomyces...

Interactions between genes and proteins are crucial for efficient processing of internal or external signals, but this connectivity also amplifies stochastic fluctuations by propagating noise components. Linear (unbranched) cascades were shown to exhibit an interplay the sensitivity changes in input signals ability buffer noise. We searched biological circuits that can maintain signaling while minimizing propagation, focusing on cases where is characterized rapid fluctuations. Negative...

Morphogen gradients are established by the localized production and subsequent diffusion of signaling molecules. It is generally assumed that cell fates induced only after morphogen profiles have reached their steady state. Yet, patterning processes during early development occur rapidly, tissue may precede convergence gradient to its Here we consider implications pre-steady-state decoding Bicoid for anterior–posterior axis Drosophila embryo. Quantitative analysis shift in expression domains...

Gene expression depends on the frequency of transcription events (burst frequency) and number mRNA molecules made per event size). Both processes are encoded in promoter sequence, yet their dependence mutations is poorly understood. Theory suggests that burst size can be distinguished by monitoring stochastic variation (noise) gene expression: Increasing will increase mean without changing noise, while increasing decrease noise. To reveal principles which sequence regulates frequency, we...

Modeling of development in the fruit fly yields an algorithm useful designing wireless communication networks.