3,117 research outputs found
Pathway-Based Genomics Prediction using Generalized Elastic Net.
We present a novel regularization scheme called The Generalized Elastic Net (GELnet) that incorporates gene pathway information into feature selection. The proposed formulation is applicable to a wide variety of problems in which the interpretation of predictive features using known molecular interactions is desired. The method naturally steers solutions toward sets of mechanistically interlinked genes. Using experiments on synthetic data, we demonstrate that pathway-guided results maintain, and often improve, the accuracy of predictors even in cases where the full gene network is unknown. We apply the method to predict the drug response of breast cancer cell lines. GELnet is able to reveal genetic determinants of sensitivity and resistance for several compounds. In particular, for an EGFR/HER2 inhibitor, it finds a possible trans-differentiation resistance mechanism missed by the corresponding pathway agnostic approach
TRACING CO-REGULATORY NETWORK DYNAMICS IN NOISY, SINGLE-CELL TRANSCRIPTOME TRAJECTORIES
The availability of gene expression data at the single cell level makes it possible to probe the molecular underpinnings of complex biological processes such as differentiation and oncogenesis. Promising new methods have emerged for reconstructing a progression 'trajectory' from static single-cell transcriptome measurements. However, it remains unclear how to adequately model the appreciable level of noise in these data to elucidate gene regulatory network rewiring. Here, we present a framework called Single Cell Inference of MorphIng Trajectories and their Associated Regulation (SCIMITAR) that infers progressions from static single-cell transcriptomes by employing a continuous parametrization of Gaussian mixtures in high-dimensional curves. SCIMITAR yields rich models from the data that highlight genes with expression and co-expression patterns that are associated with the inferred progression. Further, SCIMITAR extracts regulatory states from the implicated trajectory-evolving co-expression networks. We benchmark the method on simulated data to show that it yields accurate cell ordering and gene network inferences. Applied to the interpretation of a single-cell human fetal neuron dataset, SCIMITAR finds progression-associated genes in cornerstone neural differentiation pathways missed by standard differential expression tests. Finally, by leveraging the rewiring of gene-gene co-expression relations across the progression, the method reveals the rise and fall of co-regulatory states and trajectory-dependent gene modules. These analyses implicate new transcription factors in neural differentiation including putative co-factors for the multi-functional NFAT pathway
An experimental test of all theories with predictive power beyond quantum theory
According to quantum theory, the outcomes of future measurements cannot (in
general) be predicted with certainty. In some cases, even with a complete
physical description of the system to be measured and the measurement
apparatus, the outcomes of certain measurements are completely random. This
raises the question, originating in the paper by Einstein, Podolsky and Rosen,
of whether quantum mechanics is the optimal way to predict measurement
outcomes. Established arguments and experimental tests exclude a few specific
alternative models. Here, we provide a complete answer to the above question,
refuting any alternative theory with significantly more predictive power than
quantum theory. More precisely, we perform various measurements on distant
entangled photons, and, under the assumption that these measurements are chosen
freely, we give an upper bound on how well any alternative theory could predict
their outcomes. In particular, in the case where quantum mechanics predicts two
equally likely outcomes, our results are incompatible with any theory in which
the probability of a prediction is increased by more than ~0.19. Hence, we can
immediately refute any already considered or yet-to-be-proposed alternative
model with more predictive power than this.Comment: 13 pages, 4 figure
Information-based methods for predicting gene function from systematic gene knock-downs
<p>Abstract</p> <p>Background</p> <p>The rapid annotation of genes on a genome-wide scale is now possible for several organisms using high-throughput RNA interference assays to knock down the expression of a specific gene. To date, dozens of RNA interference phenotypes have been recorded for the nematode <it>Caenorhabditis elegans</it>. Although previous studies have demonstrated the merit of using knock-down phenotypes to predict gene function, it is unclear how the data can be used most effectively. An open question is how to optimally make use of phenotypic observations, possibly in combination with other functional genomics datasets, to identify genes that share a common role.</p> <p>Results</p> <p>We compared several methods for detecting gene-gene functional similarity from phenotypic knock-down profiles. We found that information-based measures, which explicitly incorporate a phenotype's genomic frequency when calculating gene-gene similarity, outperform non-information-based methods. We report the presence of newly predicted modules identified from an integrated functional network containing phenotypic congruency links derived from an information-based measure. One such module is a set of genes predicted to play a role in regulating body morphology based on their multiply-supported interactions with members of the TGF-<it>β </it>signaling pathway.</p> <p>Conclusion</p> <p>Information-based metrics significantly improve the comparison of phenotypic knock-down profiles, based upon their ability to enhance gene function prediction and identify novel functional modules.</p
Mutual information in random Boolean models of regulatory networks
The amount of mutual information contained in time series of two elements
gives a measure of how well their activities are coordinated. In a large,
complex network of interacting elements, such as a genetic regulatory network
within a cell, the average of the mutual information over all pairs is a
global measure of how well the system can coordinate its internal dynamics. We
study this average pairwise mutual information in random Boolean networks
(RBNs) as a function of the distribution of Boolean rules implemented at each
element, assuming that the links in the network are randomly placed. Efficient
numerical methods for calculating show that as the number of network nodes
N approaches infinity, the quantity N exhibits a discontinuity at parameter
values corresponding to critical RBNs. For finite systems it peaks near the
critical value, but slightly in the disordered regime for typical parameter
variations. The source of high values of N is the indirect correlations
between pairs of elements from different long chains with a common starting
point. The contribution from pairs that are directly linked approaches zero for
critical networks and peaks deep in the disordered regime.Comment: 11 pages, 6 figures; Minor revisions for clarity and figure format,
one reference adde
Quasiequilibrium black hole-neutron star binaries in general relativity
We construct quasiequilibrium sequences of black hole-neutron star binaries
in general relativity. We solve Einstein's constraint equations in the
conformal thin-sandwich formalism, subject to black hole boundary conditions
imposed on the surface of an excised sphere, together with the relativistic
equations of hydrostatic equilibrium. In contrast to our previous calculations
we adopt a flat spatial background geometry and do not assume extreme mass
ratios. We adopt a Gamma=2 polytropic equation of state and focus on
irrotational neutron star configurations as well as approximately nonspinning
black holes. We present numerical results for ratios of the black hole's
irreducible mass to the neutron star's ADM mass in isolation of
M_{irr}^{BH}/M_{ADM,0}^{NS} = 1, 2, 3, 5, and 10. We consider neutron stars of
baryon rest mass M_B^{NS}/M_B^{max} = 83% and 56%, where M_B^{max} is the
maximum allowed rest mass of a spherical star in isolation for our equation of
state. For these sequences, we locate the onset of tidal disruption and, in
cases with sufficiently large mass ratios and neutron star compactions, the
innermost stable circular orbit. We compare with previous results for black
hole-neutron star binaries and find excellent agreement with third-order
post-Newtonian results, especially for large binary separations. We also use
our results to estimate the energy spectrum of the outgoing gravitational
radiation emitted during the inspiral phase for these binaries.Comment: 17 pages, 15 figures, published in Phys. Rev.
A search engine to identify pathway genes from expression data on multiple organisms
<p>Abstract</p> <p>Background</p> <p>The completion of several genome projects showed that most genes have not yet been characterized, especially in multicellular organisms. Although most genes have unknown functions, a large collection of data is available describing their transcriptional activities under many different experimental conditions. In many cases, the coregulatation of a set of genes across a set of conditions can be used to infer roles for genes of unknown function.</p> <p>Results</p> <p>We developed a search engine, the Multiple-Species Gene Recommender (MSGR), which scans gene expression datasets from multiple organisms to identify genes that participate in a genetic pathway. The MSGR takes a query consisting of a list of genes that function together in a genetic pathway from one of six organisms: <it>Homo sapiens</it>, <it>Drosophila melanogaster</it>, <it>Caenorhabditis elegans</it>, <it>Saccharomyces cerevisiae</it>, <it>Arabidopsis thaliana</it>, and <it>Helicobacter pylori</it>. Using a probabilistic method to merge searches, the MSGR identifies genes that are significantly coregulated with the query genes in one or more of those organisms. The MSGR achieves its highest accuracy for many human pathways when searches are combined across species. We describe specific examples in which new genes were identified to be involved in a neuromuscular signaling pathway and a cell-adhesion pathway.</p> <p>Conclusion</p> <p>The search engine can scan large collections of gene expression data for new genes that are significantly coregulated with a pathway of interest. By integrating searches across organisms, the MSGR can identify pathway members whose coregulation is either ancient or newly evolved.</p
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