ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work

<p>Abstract</p> <p>Background</p> <p>Experimentalists are overwhelmed by high-throughput data and there is an urgent need to condense information into simple hypotheses. For example, large amounts of microarray and deep sequencing data are becoming available, describing a variety of experimental conditions such as gene knockout and knockdown, the effect of interventions, and the differences between tissues and cell lines.</p> <p>Results</p> <p>To address this challenge, we developed a method, implemented as a Cytoscape plugin called <it>ExprEssence</it>. As input we take a network of interaction, stimulation and/or inhibition links between genes/proteins, and differential data, such as gene expression data, tracking an intervention or development in time. We condense the network, highlighting those links across which the largest changes can be observed. Highlighting is based on a simple formula inspired by the law of mass action. We can interactively modify the threshold for highlighting and instantaneously visualize results. We applied <it>ExprEssence </it>to three scenarios describing kidney podocyte biology, pluripotency and ageing: 1) We identify putative processes involved in podocyte (de-)differentiation and validate one prediction experimentally. 2) We predict and validate the expression level of a transcription factor involved in pluripotency. 3) Finally, we generate plausible hypotheses on the role of apoptosis, cell cycle deregulation and DNA repair in ageing data obtained from the hippocampus.</p> <p>Conclusion</p> <p>Reducing the size of gene/protein networks to the few links affected by large changes allows to screen for putative mechanistic relationships among the genes/proteins that are involved in adaptation to different experimental conditions, yielding important hypotheses, insights and suggestions for new experiments. We note that we do not focus on the identification of 'active subnetworks'. Instead we focus on the identification of single links (which may or may not form subnetworks), and these single links are much easier to validate experimentally than submodules. <it>ExprEssence </it>is available at <url>http://sourceforge.net/projects/expressence/</url>.</p

Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers

<p>Abstract</p> <p>Background</p> <p>Experimentally validated data on gene regulation are hard to obtain. In particular, information about transcription factor binding sites in regulatory regions are scattered around in the literature. This impedes their systematic in-context analysis, e.g. the inference of their conservation in evolutionary history.</p> <p>Results</p> <p>We demonstrate the power of integrative bioinformatics by including curated transcription factor binding site information into the UCSC genome browser, using wiki and custom tracks, which enable easy publication of annotation data. Data integration allows to investigate the evolution of gene regulation of the pluripotency-associated genes Oct4, Sox2 and Nanog. For the first time, experimentally validated transcription factor binding sites in the regulatory regions of all three genes were assembled together based on manual curation of data from 39 publications. Using the UCSC genome browser, these data were then visualized in the context of multi-species conservation based on genomic alignment. We confirm previous hypotheses regarding the evolutionary age of specific regulatory patterns, establishing their "deep homology". We also confirm some other principles of Carroll's "Genetic theory of Morphological Evolution", such as "mosaic pleiotropy", exemplified by the dual role of Sox2 reflected in its regulatory region.</p> <p>Conclusions</p> <p>We were able to elucidate some aspects of the evolution of gene regulation for three genes associated with pluripotency. Based on the expected return on investment for the community, we encourage other scientists to contribute experimental data on gene regulation (original work as well as data collected for reviews) to the UCSC system, to enable studies of the evolution of gene regulation on a large scale, and to report their findings.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Gustavo Glusman and Dr. Juan Caballero, Institute for Systems Biology, Seattle, USA (nominated by Dr. Doron Lancet, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel), Dr. Niels Grabe, TIGA Center (BIOQUANT) and Medical Systems Biology Group, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Germany (nominated by Dr. Mikhail Gelfand, Department of Bioinformatics, Institute of Information Transfer Problems, Russian Academy of Science, Moscow, Russian Federation) and Dr. Franz-Josef Müller, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA, USA and University Hospital for Psychiatry and Psychotherapy (part of ZIP gGmbH), University of Kiel, Germany (nominated by Dr. Trey Ideker, University of California, San Diego, La Jolla CA, United States).</p

Isolation and characterisation of chick embryonic primordial germ cells

Embryonic stem cells (cESCs) can be isolated from chick embryos, with the ability to contribute to all somatic lineages in chimaeras, but not to the germ line. However, lines of chicken embryonic germ cells (cEGCs), which are able to contribute to the germ line, can be established from chicken primordial germ cells (cPGCs). However very little is known about these cells, or about the changes that accompany the establishment of gonadal cells as self-renewing cell lines. This thesis presents a detailed study of the properties of cPGCs and the parent tissue from which they are derived. Gene expression profiles for 30 genes related to pluripotency and/or differentiation were are compared between gonads at the indifferent stage (stage 26-28HH), in primary gonocytes, established PGCs and cESCs. The results reveal great heterogeneity in the expression of various markers in culture. Several genes associated with pluripotency change dramatically upon culture. The most salient of these changes is that while cSox3 (but not Sox2) is expressed in the gonads, whereas their expression becomes reversed upon culture (becoming more similar to mammalian stem cells). This suggests that these two SoxB1 class genes have swapped functions in chick. In the process of studying the expression pluripotency markers in later (stage HH35) gonads, we made an unexpected discovery: both male and female embryos show left-right asymmetric patterns of expression of some, but not all, of these markers. Expression of pluripotency (cPouV, cNanog, cSox2 and ERNI) in the left gonad is much higher than those in the right gonad of both sexes. The expression of pluripotency markers is irrespective of its colonisation by primordial germ cells, and it appears that this left-right decision is made independently of whether the gonad will regress or be retained. These findings offer a new model system for investigating the roles of pluripotency-related markers during normal development as well as in stem cell lines