To understand the regulation of tissue-specific gene expression, the GTEx Consortium generated RNA-seq expression data for more than thirty distinct human tissues. This data provides an opportunity ...for deriving shared and tissue specific gene regulatory networks on the basis of co-expression between genes. However, a small number of samples are available for a majority of the tissues, and therefore statistical inference of networks in this setting is highly underpowered. To address this problem, we infer tissue-specific gene co-expression networks for 35 tissues in the GTEx dataset using a novel algorithm, GNAT, that uses a hierarchy of tissues to share data between related tissues. We show that this transfer learning approach increases the accuracy with which networks are learned. Analysis of these networks reveals that tissue-specific transcription factors are hubs that preferentially connect to genes with tissue specific functions. Additionally, we observe that genes with tissue-specific functions lie at the peripheries of our networks. We identify numerous modules enriched for Gene Ontology functions, and show that modules conserved across tissues are especially likely to have functions common to all tissues, while modules that are upregulated in a particular tissue are often instrumental to tissue-specific function. Finally, we provide a web tool, available at mostafavilab.stat.ubc.ca/GNAT, which allows exploration of gene function and regulation in a tissue-specific manner.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Physiological data are routinely recorded in intensive care, but their use for rapid assessment of illness severity or long-term morbidity prediction has been limited. We developed a physiological ...assessment score for preterm newborns, akin to an electronic Apgar score, based on standard signals recorded noninvasively on admission to a neonatal intensive care unit. We were able to accurately and reliably estimate the probability of an individual preterm infant's risk of severe morbidity on the basis of noninvasive measurements. This prediction algorithm was developed with electronically captured physiological time series data from the first 3 hours of life in preterm infants (< or =34 weeks gestation, birth weight < or =2000 g). Extraction and integration of the data with state-of-the-art machine learning methods produced a probability score for illness severity, the PhysiScore. PhysiScore was validated on 138 infants with the leave-one-out method to prospectively identify infants at risk of short- and long-term morbidity. PhysiScore provided higher accuracy prediction of overall morbidity (86% sensitive at 96% specificity) than other neonatal scoring systems, including the standard Apgar score. PhysiScore was particularly accurate at identifying infants with high morbidity related to specific complications (infection: 90% at 100%; cardiopulmonary: 96% at 100%). Physiological parameters, particularly short-term variability in respiratory and heart rates, contributed more to morbidity prediction than invasive laboratory studies. Our flexible methodology of individual risk prediction based on automated, rapid, noninvasive measurements can be easily applied to a range of prediction tasks to improve patient care and resource allocation.
Genetics aims to understand the relation between genotype and phenotype. However, because complete deletion of most yeast genes (~80%) has no obvious phenotypic consequence in rich medium, it is ...difficult to study their functions. To uncover phenotypes for this nonessential fraction of the genome, we performed 1144 chemical genomic assays on the yeast whole-genome heterozygous and homozygous deletion collections and quantified the growth fitness of each deletion strain in the presence of chemical or environmental stress conditions. We found that 97% of gene deletions exhibited a measurable growth phenotype, suggesting that nearly all genes are essential for optimal growth in at least one condition.
Population genomics of human gene expression Montgomery, Stephen; Dermitzakis, Emmanouil T; Bird, Christine P ...
Nature genetics,
10/2007, Letnik:
39, Številka:
10
Journal Article
Recenzirano
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Genetic variation influences gene expression, and this variation in gene expression can be efficiently mapped to specific genomic regions and variants. Here we have used gene expression profiling of ...Epstein-Barr virus-transformed lymphoblastoid cell lines of all 270 individuals genotyped in the HapMap Consortium to elucidate the detailed features of genetic variation underlying gene expression variation. We find that gene expression is heritable and that differentiation between populations is in agreement with earlier small-scale studies. A detailed association analysis of over 2.2 million common SNPs per population (5% frequency in HapMap) with gene expression identified at least 1,348 genes with association signals in cis and at least 180 in trans. Replication in at least one independent population was achieved for 37% of cis signals and 15% of trans signals, respectively. Our results strongly support an abundance of cis-regulatory variation in the human genome. Detection of trans effects is limited but suggests that regulatory variation may be the key primary effect contributing to phenotypic variation in humans. We also explore several methodologies that improve the current state of analysis of gene expression variation.
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DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
To elucidate gene function on a global scale, we identified pairs of genes that are coexpressed over 3182 DNA microarrays from humans, flies, worms, and yeast. We found 22,163 such coexpression ...relationships, each of which has been conserved across evolution. This conservation implies that the coexpression of these gene pairs confers a selective advantage and therefore that these genes are functionally related. Many of these relationships provide strong evidence for the involvement of new genes in core biological functions such as the cell cycle, secretion, and protein expression. We experimentally confirmed the predictions implied by some of these links and identified cell proliferation functions for several genes. By assembling these links into a gene-coexpression network, we found several components that were animal-specific as well as interrelationships between newly evolved and ancient modules.
The adaptive immune system confers protection by generating a diverse repertoire of antibody receptors that are rapidly expanded and contracted in response to specific targets. Next-generation DNA ...sequencing now provides the opportunity to survey this complex and vast repertoire. In the present work, we describe a set of tools for the analysis of antibody repertoires and their application to elucidating the dynamics of the response to viral vaccination in human volunteers. By analyzing data from 38 separate blood samples across 2 y, we found that the use of the germ-line library of V and J segments is conserved between individuals over time. Surprisingly, there appeared to be no correlation between the use level of a particular VJ combination and degree of expansion. We found the antibody RNA repertoire in each volunteer to be highly dynamic, with each individual displaying qualitatively different response dynamics. By using combinatorial phage display, we screened selected VH genes paired with their corresponding VL library for affinity against the vaccine antigens. Altogether, this work presents an additional set of tools for profiling the human antibody repertoire and demonstrates characterization of the fast repertoire dynamics through time in multiple individuals responding to an immune challenge.
Despite the importance of the immune system in many diseases, there are currently no objective benchmarks of immunological health. In an effort to identifying such markers, we used influenza ...vaccination in 30 young (20–30 years) and 59 older subjects (60 to >89 years) as models for strong and weak immune responses, respectively, and assayed their serological responses to influenza strains as well as a wide variety of other parameters, including gene expression, antibodies to hemagglutinin peptides, serum cytokines, cell subset phenotypes and in vitro cytokine stimulation. Using machine learning, we identified nine variables that predict the antibody response with 84% accuracy. Two of these variables are involved in apoptosis, which positively associated with the response to vaccination and was confirmed to be a contributor to vaccine responsiveness in mice. The identification of these biomarkers provides new insights into what immune features may be most important for immune health.
A systems analysis of immune biomarkers in 89 young and older adults revealed age‐dependent and age‐independent features, including markers of apoptosis that correlated with antibody responses to a seasonal influenza vaccine.
Synopsis
A systems analysis of immune biomarkers in 89 young and older adults revealed age‐dependent and age‐independent features, including markers of apoptosis that correlated with antibody responses to a seasonal influenza vaccine.
Influenza hemagglutinin peptide arrays reveal age‐associated effects that correlate with both pre‐existing and vaccine‐induced antibody titers.
Age‐dependent and age‐independent baseline immune parameters correlate with and substantially predict the serological response to a seasonal influenza vaccine.
Soluble FasL and gene modules associated with apoptosis are predictors of the serological response to an influenza vaccine, which was abrogated in Fas‐deficient mice.
The differentiation of hematopoietic stem cells into cells of the immune system has been studied extensively in mammals, but the transcriptional circuitry that controls it is still only partially ...understood. Here, the Immunological Genome Project gene-expression profiles across mouse immune lineages allowed us to systematically analyze these circuits. To analyze this data set we developed Ontogenet, an algorithm for reconstructing lineage-specific regulation from gene-expression profiles across lineages. Using Ontogenet, we found differentiation stage-specific regulators of mouse hematopoiesis and identified many known hematopoietic regulators and 175 previously unknown candidate regulators, as well as their target genes and the cell types in which they act. Among the previously unknown regulators, we emphasize the role of ETV5 in the differentiation of γδ T cells. As the transcriptional programs of human and mouse cells are highly conserved, it is likely that many lessons learned from the mouse model apply to humans.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Broadly neutralizing HIV antibodies (bnAbs) are typically highly somatically mutated, raising doubts as to whether they can be elicited by vaccination. We used 454 sequencing and designed a novel ...phylogenetic method to model lineage evolution of the bnAbs PGT121-134 and found a positive correlation between the level of somatic hypermutation (SHM) and the development of neutralization breadth and potency. Strikingly, putative intermediates were characterized that show approximately half the mutation level of PGT121-134 but were still capable of neutralizing roughly 40-80% of PGT121-134 sensitive viruses in a 74-virus panel at median titers between 15- and 3-fold higher than PGT121-134. Such antibodies with lower levels of SHM may be more amenable to elicitation through vaccination while still providing noteworthy coverage. Binding characterization indicated a preference of inferred intermediates for native Env binding over monomeric gp120, suggesting that the PGT121-134 lineage may have been selected for binding to native Env at some point during maturation. Analysis of glycan-dependent neutralization for inferred intermediates identified additional adjacent glycans that comprise the epitope and suggests changes in glycan dependency or recognition over the course of affinity maturation for this lineage. Finally, patterns of neutralization of inferred bnAb intermediates suggest hypotheses as to how SHM may lead to potent and broad HIV neutralization and provide important clues for immunogen design.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Cells respond to environmental perturbations with changes in their gene expression that are coordinated in magnitude and time. Timing information about individual genes, rather than clusters, ...provides a refined way to view and analyze responses, but it is hard to estimate accurately. To analyze response timing of individual genes, we developed a parametric model that captures the typical temporal responses: an abrupt early response followed by a second transition to a steady state. This impulse model explicitly represents natural temporal properties such as the onset and the offset time, and can be estimated robustly, as demonstrated by its superior ability to impute missing values in gene expression data. Using response time of individual genes, we identify relations between gene function and their response timing, showing, for example, how cytosolic ribosomal genes are only repressed after the mitochondrial ribosome is activated. We further demonstrate a strong relation between the binding affinity of a transcription factor and the activation timing of its targets, suggesting that graded binding affinities could be a widely used mechanism for controlling expression timing. See online Supplementary Material at (www.liebertonline.com).
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