Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm

Peer reviewedPublisher PD

Visualizing the genome: techniques for presenting human genome data and annotations

BACKGROUND: In order to take full advantage of the newly available public human genome sequence data and associated annotations, biologists require visualization tools ("genome browsers") that can accommodate the high frequency of alternative splicing in human genes and other complexities. RESULTS: In this article, we describe visualization techniques for presenting human genomic sequence data and annotations in an interactive, graphical format. These techniques include: one-dimensional, semantic zooming to show sequence data alongside gene structures; color-coding exons to indicate frame of translation; adjustable, moveable tiers to permit easier inspection of a genomic scene; and display of protein annotations alongside gene structures to show how alternative splicing impacts protein structure and function. These techniques are illustrated using examples from two genome browser applications: the Neomorphic GeneViewer annotation tool and ProtAnnot, a prototype viewer which shows protein annotations in the context of genomic sequence. CONCLUSION: By presenting techniques for visualizing genomic data, we hope to provide interested software developers with a guide to what features are most likely to meet the needs of biologists as they seek to make sense of the rapidly expanding body of public genomic data and annotations

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

BackgroundAlternative Splicing (AS) as a post-transcription regulation mechanism is an important application of RNA-seq studies in eukaryotes. A number of software and computational methods have been developed for detecting AS. Most of the methods, however, are designed and tested on animal data, such as human and mouse. Plants genes differ from those of animals in many ways, e.g., the average intron size and preferred AS types. These differences may require different computational approaches and raise questions about their effectiveness on plant data. The goal of this paper is to benchmark existing computational differential splicing (or transcription) detection methods so that biologists can choose the most suitable tools to accomplish their goals. ResultsThis study compares the eight popular public available software packages for differential splicing analysis using both simulated and real Arabidopsis thaliana RNA-seq data. All software are freely available. The study examines the effect of varying AS ratio, read depth, dispersion pattern, AS types, sample sizes and the influence of annotation. Using a real data, the study looks at the consistences between the packages and verifies a subset of the detected AS events using PCR studies. ConclusionsNo single method performs the best in all situations. The accuracy of annotation has a major impact on which method should be chosen for AS analysis. DEXSeq performs well in the simulated data when the AS signal is relative strong and annotation is accurate. Cufflinks achieve a better tradeoff between precision and recall and turns out to be the best one when incomplete annotation is provided. Some methods perform inconsistently for different AS types. Complex AS events that combine several simple AS events impose problems for most methods, especially for MATS. MATS stands out in the analysis of real RNA-seq data when all the AS events being evaluated are simple AS events

Prevalence of alternative splicing choices in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>Around 14% of protein-coding genes of <it>Arabidopsis thaliana </it>genes from the TAIR9 genome release are annotated as producing multiple transcript variants through alternative splicing. However, for most alternatively spliced genes in <it>Arabidopsis</it>, the relative expression level of individual splicing variants is unknown.</p> <p>Results</p> <p>We investigated prevalence of alternative splicing (AS) events in <it>Arabidopsis thaliana </it>using ESTs. We found that for most AS events with ample EST coverage, the majority of overlapping ESTs strongly supported one major splicing choice, with less than 10% of ESTs supporting the minor form. Analysis of ESTs also revealed a small but noteworthy subset of genes for which alternative choices appeared with about equal prevalence, suggesting that for these genes the variant splicing forms co-occur in the same cell types. Of the AS events in which both forms were about equally prevalent, more than 80% affected untranslated regions or involved small changes to the encoded protein sequence.</p> <p>Conclusions</p> <p>Currently available evidence from ESTs indicates that alternative splicing in <it>Arabidopsis </it>occurs and affects many genes, but for most genes with documented alternative splicing, one AS choice predominates. To aid investigation of the role AS may play in modulating function of <it>Arabidopsis </it>genes, we provide an on-line resource (ArabiTag) that supports searching AS events by gene, by EST library keyword search, and by relative prevalence of minor and major forms.</p

Citizen innovation: DIY design and the Thames water turbine

“When electricity prices prevent older people from heating their homes, and the River Thames is just down the road, why are we not using it to power our city?” was a question posed by a member of the Geezers Club at an AgeUK centre in East London. The Geezers are a group of older men aged from 55 to late 80’s, who meet weekly in Tower Hamlets. For the last five years they have been working with artist Loraine Leeson, engineer Toby Borland and others to realise their dream of using the River Thames to provide energy for London’s riverside communities. The project was initiated by an art commission responding to the Democratising Technology research project being carried out by Ann Light and others at Queen Mary University of London that questioned why the extensive life experience of older people was failing to inform new developments in technology. Members of the Geezers group were able to recollect developments in tidal and wave power from years earlier, many of which were brought to a premature end in the 1980’s. Though research into energy from wind turbines did re-commence, the power of the Thames remains relatively untapped to this day. During the life of the project Active Energy has involved a practical proposal for installing tidal turbines at the Thames Barrier, renewable energy workshops at a local school, a wind-driven public light-work for the roof of an Age UK centre, prototyping workshops at University of East London and art exhibitions in both the UK and USA that have brought these issues to public attention. The most recent phase of the project has been to create an ultra low-cost turbine to produce energy from the river and prompt a debate on the use of the River Thames as a source of energy for the city. The process of creative facilitation that has driven this work and fostered citizen-led innovation by older people has gained international attention, whilst the small scale turbine that has been designed specifically for slow moving tidal rivers is thought to be the first of its kind and capable of low-cost replication for developing nations overseas

Prospectus, April 20, 1988

https://spark.parkland.edu/prospectus_1988/1014/thumbnail.jp

Prospectus, October 15, 1986

https://spark.parkland.edu/prospectus_1986/1025/thumbnail.jp

Prospectus, April 22, 1987

https://spark.parkland.edu/prospectus_1987/1013/thumbnail.jp

Identification of Cytokinin-Responsive Genes Using Microarray Meta-Analysis and RNA-Seq in Arabidopsis

Cytokinins are N6-substituted adenine derivatives that play diverse roles in plant growth and development. We sought to define a robust set of genes regulated by cytokinin as well as to query the response of genes not represented on microarrays. To this end, we performed a meta-analysis of microarray data from a variety of cytokinin-treated samples and used RNA-seq to examine cytokinin-regulated gene expression in Arabidopsis (Arabidopsis thaliana). Microarray meta-analysis using 13 microarray experiments combined with empirically defined filtering criteria identified a set of 226 genes differentially regulated by cytokinin, a subset of which has previously been validated by other methods. RNA-seq validated about 73% of the up-regulated genes identified by this meta-analysis. In silico promoter analysis indicated an overrepresentation of type-B Arabidopsis response regulator binding elements, consistent with the role of type-B Arabidopsis response regulators as primary mediators of cytokinin-responsive gene expression. RNA-seq analysis identified 73 cytokinin-regulated genes that were not represented on the ATH1 microarray. Representative genes were verified using quantitative reverse transcription-polymerase chain reaction and NanoString analysis. Analysis of the genes identified reveals a substantial effect of cytokinin on genes encoding proteins involved in secondary metabolism, particularly those acting in flavonoid and phenylpropanoid biosynthesis, as well as in the regulation of redox state of the cell, particularly a set of glutaredoxin genes. Novel splicing events were found in members of some gene families that are known to play a role in cytokinin signaling or metabolism. The genes identified in this analysis represent a robust set of cytokinin-responsive genes that are useful in the analysis of cytokinin function in plants

Prospectus, November 11, 1987

https://spark.parkland.edu/prospectus_1987/1024/thumbnail.jp