http://www.dspace.cam.ac.uk:80/handle/1810/227507 Thu, 23 May 2013 12:44:49 GMT 2013-05-23T12:44:49Z http://www.dspace.cam.ac.uk:80/handle/1810/244335 Title: Following the assembly of functional circuitry: high resolution large-scale population neuronal dynamics in the neonatal mouse retina Authors: Maccione, Alessandro; Hennig, Matthias H.; Gandolfo, Mauro; Muthmann, Oliver; Down, Matthew; van Coppenhagen, James; Jones, Alyssa; Eglen, Stephen J.; Berdondini, L; Sernagor, E Tue, 01 Jan 2013 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244335 2013-01-01T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/240702 Title: When are microcircuits well-modeled by maximum entropy methods? Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Mon, 19 Jul 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/240702 2010-07-19T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238513 Title: Analysis of simultaneous multielectrode recordings with 4,096 channels: changing dynamics of spontaneous activity in the developing retina Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Sun, 17 Jul 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238513 2011-07-17T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238347 Title: A simple Bayesian estimate of direct RNAi gene regulation events from differential gene expression profiles Authors: Wilson, Paul A; Plucinski, Mathew Abstract: Abstract Background Microarrays are commonly used to investigate both the therapeutic potential and functional effects of RNA interfering (RNAi) oligonucleotides such as microRNA (miRNA) and small interfering RNA (siRNA). However, the resulting datasets are often challenging to interpret as they include extensive information relating to both indirect transcription effects and off-target interference events. Method In an attempt to refine the utility of microarray expression data when evaluating the direct transcriptional affects of an RNAi agent we have developed SBSE (Simple Bayesian Seed Estimate). The key assumption implemented in SBSE is that both direct regulation of transcription by miRNA, and siRNA off-target interference, can be estimated using the differential distribution of an RNAi sequence (seed) motif in a ranked 3' untranslated region (3' UTR) sequence repository. SBSE uses common microarray summary statistics (i.e. fold change) and a simple Bayesian analysis to estimate how the RNAi agent dictated the observed differential expression profile. On completion a trace of the estimate and the location of the optimal partitioning of the dataset are plotted within a simple graphical representation of the 3'UTR landscape. The combined estimates define the differential distribution of the query motif within the dataset and by inference are used to quantify the magnitude of the direct RNAi transcription effect. Results SBSE has been evaluated using five diverse human RNAi microarray focused investigations. In each instance SBSE unambiguously identified the most likely location of the direct RNAi effects for each of the differential gene expression profiles. Conclusion These analyses indicate that miRNA with conserved seed regions may share minimal biological activity and that SBSE can be used to differentiate siRNAs of similar efficacy but with different off-target signalling potential. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 19 May 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238347 2011-05-19T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238213 Title: Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes Authors: Curtis, Christina; Landis, Gary N; Folk, Donna; Wehr, Nancy B; Hoe, Nicholas; Waskar, Morris; Abdueva, Diana; Skvortsov, Dmitriy; Ford, Daniel; Luu, Allan; Badrinath, Ananth; Levine, Rodney L; Bradley, Timothy J; Tavare, Simon; Tower, John Abstract: Abstract Background Several interventions increase lifespan in model organisms, including reduced insulin/insulin-like growth factor-like signaling (IIS), FOXO transcription factor activation, dietary restriction, and superoxide dismutase (SOD) over-expression. One question is whether these manipulations function through different mechanisms, or whether they intersect on common processes affecting aging. Results A doxycycline-regulated system was used to over-express manganese-SOD (MnSOD) in adult Drosophila, yielding increases in mean and maximal lifespan of 20%. Increased lifespan resulted from lowered initial mortality rate and required MnSOD over-expression in the adult. Transcriptional profiling indicated that the expression of specific genes was altered by MnSOD in a manner opposite to their pattern during normal aging, revealing a set of candidate biomarkers of aging enriched for carbohydrate metabolism and electron transport genes and suggesting a true delay in physiological aging, rather than a novel phenotype. Strikingly, cross-dataset comparisons indicated that the pattern of gene expression caused by MnSOD was similar to that observed in long-lived Caenorhabditis elegans insulin-like signaling mutants and to the xenobiotic stress response, thus exposing potential conserved longevity promoting genes and implicating detoxification in Drosophila longevity. Conclusion The data suggest that MnSOD up-regulation and a retrograde signal of reactive oxygen species from the mitochondria normally function as an intermediate step in the extension of lifespan caused by reduced insulin-like signaling in various species. The results implicate a species-conserved net of coordinated genes that affect the rate of senescence by modulating energetic efficiency, purine biosynthesis, apoptotic pathways, endocrine signals, and the detoxification and excretion of metabolites. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Sun, 09 Dec 2007 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238213 2007-12-09T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238028 Title: Using expression arrays for copy number detection: an example from E. Coli Authors: Skvortsov, Dmitriy; Abdueva, Diana; Stitzer, Michael E; Finkel, Steven E; Tavare, Simon Abstract: Abstract Background The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations. While many of the methods and algorithms developed for the analysis microarrays have focused on expression analysis, the same technology can be used to detect genetic alterations, using for example standard commercial Affymetrix arrays. Due to the nature of the resultant data, standard techniques for processing GeneChip expression experiments are inapplicable. Results We have developed a robust and flexible methodology for high-resolution analysis of DNA copy number of whole genomes, using Affymetrix high-density expression oligonucleotide microarrays. Copy number is obtained from fluorescence signals after processing with novel normalization, spatial artifact correction, data transformation and deletion/duplication detection. We applied our approach to identify deleted and amplified regions in E. coli mutants obtained after prolonged starvation. Conclusion The availability of Affymetrix expression chips for a wide variety of organisms makes the proposed array CGH methodology useful more generally. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 13 Jun 2007 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238028 2007-06-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237614 Title: High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta Authors: Daelemans, Caroline; Ritchie, Matthew E; Smits, Guillaume; Abu-Amero, Sayeda; Sudbery, Ian M; Forrest, Matthew S; Campino, Susana; Clark, Taane G; Stanier, Philip; Kwiatkowski, Dominic; Deloukas, Panos; Dermitzakis, Emmanouil T; Tavare, Simon; Moore, Gudrun E; Dunham, Ian Abstract: Abstract Background Imprinted genes show expression from one parental allele only and are important for development and behaviour. This extreme mode of allelic imbalance has been described for approximately 56 human genes. Imprinting status is often disrupted in cancer and dysmorphic syndromes. More subtle variation of gene expression, that is not parent-of-origin specific, termed 'allele-specific gene expression' (ASE) is more common and may give rise to milder phenotypic differences. Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue. Results Twenty-three family trios of placental cDNA, placental genomic DNA (gDNA) and gDNA from both parents were tested for 130 candidate genes with the Sequenom MassArray system. Six genes were found differentially expressed but none imprinted. The Illumina ASE BeadArray platform was then used to test 1536 SNPs in 932 genes. The array was enriched for the human orthologues of 124 mouse candidate genes from bioinformatics predictions and 10 human candidate imprinted genes from EST database mining. After quality control pruning, a total of 261 informative SNPs (214 genes) remained for analysis. Imprinting with maternal expression was demonstrated for the lymphocyte imprinted gene ZNF331 in human placenta. Two potential differentially methylated regions (DMRs) were found in the vicinity of ZNF331. None of the bioinformatically predicted candidates tested showed imprinting except for a skewed allelic expression in a parent-specific manner observed for PHACTR2, a neighbour of the imprinted PLAGL1 gene. ASE was detected for two or more individuals in 39 candidate genes (18%). Conclusions Both Sequenom and Illumina assays were sensitive enough to study imprinting and strong allelic bias. Previous bioinformatics approaches were not predictive of new imprinted genes in the human term placenta. ZNF331 is imprinted in human term placenta and might be a new ubiquitously imprinted gene, part of a primate-specific locus. Demonstration of partial imprinting of PHACTR2 calls for re-evaluation of the allelic pattern of expression for the PHACTR2-PLAGL1 locus. ASE was common in human term placenta. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Sun, 18 Apr 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237614 2010-04-18T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237612 Title: Data analysis issues for allele-specific expression using Illumina's GoldenGate assay Authors: Ritchie, Matthew E; Forrest, Matthew S; Dimas, Antigone S; Daelemans, Caroline; Dermitzakis, Emmanouil T; Deloukas, Panagiotis; Tavare, Simon Abstract: Abstract Background High-throughput measurement of allele-specific expression (ASE) is a relatively new and exciting application area for array-based technologies. In this paper, we explore several data sets which make use of Illumina's GoldenGate BeadArray technology to measure ASE. This platform exploits coding SNPs to obtain relative expression measurements for alleles at approximately 1500 positions in the genome. Results We analyze data from a mixture experiment where genomic DNA samples from pairs of individuals of known genotypes are pooled to create allelic imbalances at varying levels for the majority of SNPs on the array. We observe that GoldenGate has less sensitivity at detecting subtle allelic imbalances (around 1.3 fold) compared to extreme imbalances, and note the benefit of applying local background correction to the data. Analysis of data from a dye-swap control experiment allowed us to quantify dye-bias, which can be reduced considerably by careful normalization. The need to filter the data before carrying out further downstream analysis to remove non-responding probes, which show either weak, or non-specific signal for each allele, was also demonstrated. Throughout this paper, we find that a linear model analysis of the data from each SNP is a flexible modelling strategy that allows for testing of allelic imbalances in each sample when replicate hybridizations are available. Conclusions Our analysis shows that local background correction carried out by Illumina's software, together with quantile normalization of the red and green channels within each array, provides optimal performance in terms of false positive rates. In addition, we strongly encourage intensity-based filtering to remove SNPs which only measure non-specific signal. We anticipate that a similar analysis strategy will prove useful when quantifying ASE on Illumina's higher density Infinium BeadChips. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Tue, 25 May 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237612 2010-05-25T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237594 Title: Response to mTOR inhibition: activity of eIF4E predicts sensitivity in cell lines and acquired changes in eIF4E regulation in breast cancer Authors: Satheesha, Sampoorna; Cookson, Victoria J; Coleman, Louise J; Ingram, Nicola; Madhok, Brijesh; Hanby, Andrew M; Suleman, Charlotte A B; Sabine, Vicky S; Macaskill, E Jane; Bartlett, John M S; Dixon, J Michael; McElwaine, Jim N; Hughes, Thomas A Abstract: Abstract Background Inhibitors of the kinase mTOR, such as rapamycin and everolimus, have been used as cancer therapeutics with limited success since some tumours are resistant. Efforts to establish predictive markers to allow selection of patients with tumours likely to respond have centred on determining phosphorylation states of mTOR or its targets 4E-BP1 and S6K in cancer cells. In an alternative approach we estimated eIF4E activity, a key effector of mTOR function, and tested the hypothesis that eIF4E activity predicts sensitivity to mTOR inhibition in cell lines and in breast tumours. Results We found a greater than three fold difference in sensitivity of representative colon, lung and breast cell lines to rapamycin. Using an assay to quantify influences of eIF4E on the translational efficiency specified by structured 5'UTRs, we showed that this estimate of eIF4E activity was a significant predictor of rapamycin sensitivity, with higher eIF4E activities indicative of enhanced sensitivity. Surprisingly, non-transformed cell lines were not less sensitive to rapamycin and did not have lower eIF4E activities than cancer lines, suggesting the mTOR/4E-BP1/eIF4E axis is deregulated in these non-transformed cells. In the context of clinical breast cancers, we estimated eIF4E activity by analysing expression of eIF4E and its functional regulators within tumour cells and combining these scores to reflect inhibitory and activating influences on eIF4E. Estimates of eIF4E activity in cancer biopsies taken at diagnosis did not predict sensitivity to 11-14 days of pre-operative everolimus treatment, as assessed by change in tumour cell proliferation from diagnosis to surgical excision. However, higher pre-treatment eIF4E activity was significantly associated with dramatic post-treatment changes in expression of eIF4E and 4E-binding proteins, suggesting that eIF4E is further deregulated in these tumours in response to mTOR inhibition. Conclusions Estimates of eIF4E activity predict sensitivity to mTOR inhibition in cell lines but breast tumours with high estimated eIF4E activity gain changes in eIF4E regulation in order to enhance resistance. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Mon, 14 Feb 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237594 2011-02-14T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237569 Title: Analysis of spontaneous activity patterns in developing retina: algorithms and results Abstract: Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Sun, 12 Jul 2009 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237569 2009-07-12T23:00:00Z