Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos

Sense and antisense transcripts and primers chosen for validation of RNA-Seq-based expression level changes. Sense and antisense transcripts are shown with the corresponding annotation, primer pairs used for qPCR, time points of differential expression, and notes on the presence of additional melt curve peaks. (PPTX 39 kb

XcisClique: analysis of regulatory bicliques

BACKGROUND: Modeling of cis-elements or regulatory motifs in promoter (upstream) regions of genes is a challenging computational problem. In this work, set of regulatory motifs simultaneously present in the promoters of a set of genes is modeled as a biclique in a suitably defined bipartite graph. A biologically meaningful co-occurrence of multiple cis-elements in a gene promoter is assessed by the combined analysis of genomic and gene expression data. Greater statistical significance is associated with a set of genes that shares a common set of regulatory motifs, while simultaneously exhibiting highly correlated gene expression under given experimental conditions. METHODS: XcisClique, the system developed in this work, is a comprehensive infrastructure that associates annotated genome and gene expression data, models known cis-elements as regular expressions, identifies maximal bicliques in a bipartite gene-motif graph; and ranks bicliques based on their computed statistical significance. Significance is a function of the probability of occurrence of those motifs in a biclique (a hypergeometric distribution), and on the new sum of absolute values statistic (SAV) that uses Spearman correlations of gene expression vectors. SAV is a statistic well-suited for this purpose as described in the discussion. RESULTS: XcisClique identifies new motif and gene combinations that might indicate as yet unidentified involvement of sets of genes in biological functions and processes. It currently supports Arabidopsis thaliana and can be adapted to other organisms, assuming the existence of annotated genomic sequences, suitable gene expression data, and identified regulatory motifs. A subset of Xcis Clique functionalities, including the motif visualization component MotifSee, source code, and supplementary material are available at

The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison

BACKGROUND: Analysis of DNA microarray data takes as input spot intensity measurements from scanner software and returns differential expression of genes between two conditions, together with a statistical significance assessment. This process typically consists of two steps: data normalization and identification of differentially expressed genes through statistical analysis. The Expresso microarray experiment management system implements these steps with a two-stage, log-linear ANOVA mixed model technique, tailored to individual experimental designs. The complement of tools in TM4, on the other hand, is based on a number of preset design choices that limit its flexibility. In the TM4 microarray analysis suite, normalization, filter, and analysis methods form an analysis pipeline. TM4 computes integrated intensity values (IIV) from the average intensities and spot pixel counts returned by the scanner software as input to its normalization steps. By contrast, Expresso can use either IIV data or median intensity values (MIV). Here, we compare Expresso and TM4 analysis of two experiments and assess the results against qRT-PCR data. RESULTS: The Expresso analysis using MIV data consistently identifies more genes as differentially expressed, when compared to Expresso analysis with IIV data. The typical TM4 normalization and filtering pipeline corrects systematic intensity-specific bias on a per microarray basis. Subsequent statistical analysis with Expresso or a TM4 t-test can effectively identify differentially expressed genes. The best agreement with qRT-PCR data is obtained through the use of Expresso analysis and MIV data. CONCLUSION: The results of this research are of practical value to biologists who analyze microarray data sets. The TM4 normalization and filtering pipeline corrects microarray-specific systematic bias and complements the normalization stage in Expresso analysis. The results of Expresso using MIV data have the best agreement with qRT-PCR results. In one experiment, MIV is a better choice than IIV as input to data normalization and statistical analysis methods, as it yields as greater number of statistically significant differentially expressed genes; TM4 does not support the choice of MIV input data. Overall, the more flexible and extensive statistical models of Expresso achieve more accurate analytical results, when judged by the yardstick of qRT-PCR data, in the context of an experimental design of modest complexity

Studying the Functional Genomics of Stress Responses in Loblolly Pine With the Expresso Microarray Experiment Management System

Conception, design, and implementation of cDNA microarray experiments present a variety of bioinformatics challenges for biologists and computational scientists. The multiple stages of data acquisition and analysis have motivated the design of Expresso, a system for microarray experiment management. Salient aspects of Expresso include support for clone replication and randomized placement; automatic gridding, extraction of expression data from each spot, and quality monitoring; flexible methods of combining data from individual spots into information about clones and functional categories; and the use of inductive logic programming for higher-level data analysis and mining. The development of Expresso is occurring in parallel with several generations of microarray experiments aimed at elucidating genomic responses to drought stress in loblolly pine seedlings. The current experimental design incorporates 384 pine cDNAs replicated and randomly placed in two specific microarray layouts. We describe the design of Expresso as well as results of analysis with Expresso that suggest the importance of molecular chaperones and membrane transport proteins in mechanisms conferring successful adaptation to long-term drought stress

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services

Revisiting the Gaia Hypothesis: Maximum Entropy, Kauffman’s ‘Fourth Law’ and Physiosemeiosis

Recently, Kleidon suggested to analyze Gaia as a non-equilibrium thermodynamic system that continuously moves away from equilibrium, driven by maximum entropy production which materializes in hierarchically coupled mechanisms of energetic flows via dissipation and physical work. I relate this view with Kauffman's 'Fourth Law of Thermodynamics', which I interprete as a proposition about the accumulation of information in evolutionary processes. The concept of physical work is expanded to including work directed at the capacity to work: I offer a twofold specification of Kauffman's concept of an 'autonomous agent', one as a 'self-referential heat engine', and the other in terms of physiosemeiosis, which is a naturalized application of Peirce's theory of signs. The conjunction of these three theoretical sources, Maximum Entropy, Kauffman's Fourth Law, and physiosemeiosis, shows that the Kleidon restatement of the Gaia hypothesis is equivalent to the proposition that the biosphere is generating, processing and storing information, thus directly treating information as a physical phenomenon. There is a fundamental ontological continuity between the biological processes and the human economy, as both are seen as information processing and entropy producing systems. Knowledge and energy are not substitutes, with energy and information being two aspects of the same underlying physical process

The Colonizers and Their Colonized

This study is concerned with the Self/Other dichotomy, originally formulated by scholars of South Asian history in the context of European imperialistic treatments of the peoples whom they colonized for centuries, as applied to Mexican history. I have chosen some visual, cinematic, and literary representations of indigenous and other dispossessed peoples from both colonial and post-colonial Mexico in order to gain some insights into the vision of the powerless, (the 'Other'), held by the powerful (the colonizers, whether internal or external), especially, but not exclusively, in the context of race. Some public and private works of Mexican art from the 18th , 19th. and the 20th centuries are used to understand the perceptions of the Other in Colonial Mexico City, at the time of Independence, in state-sponsored pre and post-Revolutionary spectacles representing indigenous peoples, cinematic representations of the marginalized and the dispossessed from the Golden Age of Mexican cinema, and in the representation of the marginalized in the literary and photographic works of Juan Rulfo. I conclude that an ambivalent mixture co-existed in Mexican culture through the centuries, on the one hand, honoring the blending that is expressed in the word 'mestizaje', and on the other, adhering to a thoroughly Eurocentric world view. This ambivalence persisted from the 18th century through Independence and the Revolution and its aftermath, albeit in transformed 'M. A.Mexico presents an interesting contrast to the United States with respect to the history of race since colonization. The 16th century Spanish conquerors, and the colonizers who followed them, acknowledged the offspring of their unions with indigenous women, setting a tradition that resulted, by the 20th century, in mixed race peoples becoming the major component of the Mexican population. Despite this, there remained a sense in the culture that Europe and those of European descent were still the ideal towards which Mexico aspired, while from time to time, there were paradoxical displays, honoring the ethnic diversity that was New Spanish/Mexican reality. In light of this ambivalence, I have examined some literary and artistic examples of the perception of the colonizers, internal or external, of those whom they marginalized