David M. Budden

Predictive modelling of gene expression from transcriptional regulatory elements

Predictive modelling of gene expression provides a powerful framework for exploring the regulatory logic underpinning transcriptional regulation. Recent studies have demonstrated the utility of such models in identifying dysregulation of gene and miRNA expression associated with abnormal patterns of transcription factor (TF) binding or nucleosomal histone modifications (HMs). Despite the growing popularity of such approaches, a comparative review of the various modelling algorithms and feature extraction methods is lacking. We define and compare three methods of quantifying pairwise gene-TF/HM interactions and discuss their suitability for integrating the heterogeneous chromatin immunoprecipitation (ChIP)-seq binding patterns exhibited by TFs and HMs. We then construct log-linear and ϵ-support vector regression models from various mouse embryonic stem cell (mESC) and human lymphoblastoid (GM12878) data sets, considering both ChIP-seq- and position weight matrix- (PWM)-derived in silico TF-binding. The two algorithms are evaluated both in terms of their modelling prediction accuracy and ability to identify the established regulatory roles of individual TFs and HMs. Our results demonstrate that TF-binding and HMs are highly predictive of gene expression as measured by mRNA transcript abundance, irrespective of algorithm or cell type selection and considering both ChIP-seq and PWM-derived TF-binding. As we encourage other researchers to explore and develop these results, our framework is implemented using open-source software and made available as a preconfigured bootable virtual environment.

Predicting expression: the complementary power of histone modification and transcription factor binding data

BackgroundTranscription factors (TFs) and histone modifications (HMs) play critical roles in gene expression by regulating mRNA transcription. Modelling frameworks have been developed to integrate high-throughput omics data, with the aim of elucidating the regulatory logic that results from the interactions of DNA, TFs and HMs. These models have yielded an unexpected and poorly understood result: that TFs and HMs are statistically redundant in explaining mRNA transcript abundance at a genome-wide level.ResultsWe constructed predictive models of gene expression by integrating RNA-sequencing, TF and HM chromatin immunoprecipitation sequencing and DNase I hypersensitivity data for two mammalian cell types. All models identified genome-wide statistical redundancy both within and between TFs and HMs, as previously reported. To investigate potential explanations, groups of genes were constructed for ontology-classified biological processes. Predictive models were constructed for each process to explore the distribution of statistical redundancy. We found significant variation in the predictive capacity of TFs and HMs across these processes and demonstrated the predictive power of HMs to be inversely proportional to process enrichment for housekeeping genes.ConclusionsIt is well established that the roles played by TFs and HMs are not functionally redundant. Instead, we attribute the statistical redundancy reported in this and previous genome-wide modelling studies to the heterogeneous distribution of HMs across chromatin domains. Furthermore, we conclude that statistical redundancy between individual TFs can be readily explained by nucleosome-mediated cooperative binding. This could possibly help the cell confer regulatory robustness by rejecting signalling noise and allowing control via multiple pathways.

Virtual Reference Environments: a simple way to make research reproducible

‘Reproducible research’ has received increasing attention over the past few years as bioinformatics and computational biology methodologies become more complex. Although reproducible research is progressing in several valuable ways, we suggest that recent increases in internet bandwidth and disk space, along with the availability of open-source and free-software licences for tools, enable another simple step to make research reproducible. In this article, we urge the creation of minimal virtual reference environments implementing all the tools necessary to reproduce a result, as a standard part of publication. We address potential problems with this approach, and show an example environment from our own work.

A Global Social Media Survey of Attitudes to Human Genome Editing

Ongoing breakthroughs with CRISPR/Cas-based editing could potentially revolutionize modern medicine, but there are many questions to resolve about the ethical implications for its therapeutic application. We conducted a worldwide online survey of over 12,000 people recruited via social media to gauge attitudes toward this technology and discuss our findings here.

Unsupervised recognition of salient colour for real-time image processing

Humans have the subconscious ability to create simple abstractions from observations of their physical environment. The ability to consider the colour of an object in terms of “red” or “blue”, rather than spatial distributions of reflected light wavelengths, is vital in processing and communicating information about important features within our local environment. The real-time identification of such features in image processing necessitates the software implementation of such a process; segmenting an image into regions of salient colour, and in doing so reducing the information stored and processed from 3-dimensional pixel values to a simple colour class label. This paper details a method by which colour segmentation may be performed offline and stored in a static look-up table, allowing for constant time dimensionality reduction in an arbitrary environment of coloured features. The machine learning framework requires no human supervision, and its performance is evaluated in terms of feature classification performance within a RoboCup robot soccer environment. The developed system is demonstrated to yield an 8% improvement over slower traditional methods of manual colour mapping.

NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks

Summary: The wide variety of published approaches for the problem of regulatory network inference makes using multiple inference algorithms complex and time-consuming. Network Analysis and Inference Library (NAIL) is a set of software tools to simplify the range of computational activities involved in regulatory network inference. It uses a modular approach to connect different network inference algorithms to the same visualization and network-based analyses. NAIL is technologyindependent and includes an interface layer to allow easy integration of components into other applications. Availability and implementation: NAIL is implemented in MATLAB, runs on Windows, Linux and OSX, and is available from SourceForge at https://sourceforge.net/projects/nailsystemsbiology/ for all researchers

Simulation Leagues: Analysis of Competition Formats

The selection of an appropriate competition format is critical for both the success and credibility of any competition, both real and simulated. In this paper, the automated parallelism offered by the RoboCupSoccer 2D simulation league is leveraged to conduct a 28,000 game round-robin between the top 8 teams from RoboCup 2012 and 2013. A proposed new competition format is found to reduce variation from the resultant statistically significant team performance rankings by 75 % and 67 %, when compared to the actual competition results from RoboCup 2012 and 2013 respectively. These results are statistically validated by generating 10,000 random tournaments for each of the three considered formats and comparing the respective distributions of ranking discrepancy.

RoboCup Simulation Leagues: Enabling Replicable and Robust Investigation of Complex Robotic Systems

Physically realistic simulated environments are powerful platforms for enabling measurable, replicable, and statistically robust investigation of complex robotic systems. Such environments are epitomized by the RoboCup (RC) simulation leagues, which have been successfully utilized to conduct massively parallel experiments on a variety of topics, including optimization of bipedal locomotion, self-localization from noisy perception data, and planning complex multiagent strategies without direct agent-to-agent communication. Many of these systems are later transferred to physical robots, making the simulation leagues invaluable beyond the scope of simulated soccer matches.

Modelling the conditional regulatory activity of methylated and bivalent promoters

BackgroundPredictive modelling of gene expression is a powerful framework for the in silico exploration of transcriptional regulatory interactions through the integration of high-throughput -omics data. A major limitation of previous approaches is their inability to handle conditional interactions that emerge when genes are subject to different regulatory mechanisms. Although chromatin immunoprecipitation-based histone modification data are often used as proxies for chromatin accessibility, the association between these variables and expression often depends upon the presence of other epigenetic markers (e.g. DNA methylation or histone variants). These conditional interactions are poorly handled by previous predictive models and reduce the reliability of downstream biological inference.ResultsWe have previously demonstrated that integrating both transcription factor and histone modification data within a single predictive model is rendered ineffective by their statistical redundancy. In this study, we evaluate four proposed methods for quantifying gene-level DNA methylation levels and demonstrate that inclusion of these data in predictive modelling frameworks is also subject to this critical limitation in data integration. Based on the hypothesis that statistical redundancy in epigenetic data is caused by conditional regulatory interactions within a dynamic chromatin context, we construct a new gene expression model which is the first to improve prediction accuracy by unsupervised identification of latent regulatory classes. We show that DNA methylation and H2A.Z histone variant data can be interpreted in this way to identify and explore the signatures of silenced and bivalent promoters, substantially improving genome-wide predictions of mRNA transcript abundance and downstream biological inference across multiple cell lines.ConclusionsPrevious models of gene expression have been applied successfully to several important problems in molecular biology, including the discovery of transcription factor roles, identification of regulatory elements responsible for differential expression patterns and comparative analysis of the transcriptome across distant species. Our analysis supports our hypothesis that statistical redundancy in epigenetic data is partially due to conditional relationships between these regulators and gene expression levels. This analysis provides insight into the heterogeneous roles of H3K4me3 and H3K27me3 in the presence of the H2A.Z histone variant (implicated in cancer progression) and how these signatures change during lineage commitment and carcinogenesis.

Information theoretic approaches for inference of biological networks from continuous-valued data

BackgroundCharacterising programs of gene regulation by studying individual protein-DNA and protein-protein interactions would require a large volume of high-resolution proteomics data, and such data are not yet available. Instead, many gene regulatory network (GRN) techniques have been developed, which leverage the wealth of transcriptomic data generated by recent consortia to study indirect, gene-level relationships between transcriptional regulators. Despite the popularity of such methods, previous methods of GRN inference exhibit limitations that we highlight and address through the lens of information theory.ResultsWe introduce new model-free and non-linear information theoretic measures for the inference of GRNs and other biological networks from continuous-valued data. Although previous tools have implemented mutual information as a means of inferring pairwise associations, they either introduce statistical bias through discretisation or are limited to modelling undirected relationships. Our approach overcomes both of these limitations, as demonstrated by a substantial improvement in empirical performance for a set of 160 GRNs of varying size and topology.ConclusionsThe information theoretic measures described in this study yield substantial improvements over previous approaches (e.g. ARACNE) and have been implemented in the latest release of NAIL (Network Analysis and Inference Library). However, despite the theoretical and empirical advantages of these new measures, they do not circumvent the fundamental limitation of indeterminacy exhibited across this class of biological networks. These methods have presently found value in computational neurobiology, and will likely gain traction for GRN analysis as the volume and quality of temporal transcriptomics data continues to improve.