Unequal group variances in microarray data analyses

Motivation: In searching for differentially expressed (DE) genesin microarray data, we often observe a fraction of the genesto have unequal variability between groups. This is not an issuein large samples, where a valid test exists that uses individualvariances separately. The problem arises in the small-samplesetting, where the approximately valid Welch test lacks sensitivity,while the more sensitive moderated t-test assumes equal variance. Methods: We introduce a moderated Welch test (MWT) that allowsunequal variance between groups. It is based on (i) weightingof pooled and unpooled standard errors and (ii) improved estimationof the gene-level variance that exploits the information fromacross the genes. Results: When a non-trivial proportion of genes has unequalvariability, false discovery rate (FDR) estimates based on thestandard t and moderated t-tests are often too optimistic, whilethe standard Welch test has low sensitivity. The MWT is shownto (i) perform better than the standard t, the standard Welchand the moderated t-tests when the variances are unequal betweengroups and (ii) perform similarly to the moderated t, and betterthan the standard t and Welch tests when the group variancesare equal. These results mean that MWT is more reliable thanother existing tests over wider range of data conditions. Availability: R package to perform MWT is available at http://www.meb.ki.se/~yudpaw Contact: yudi.pawitan{at}ki.se Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop     

Hardarson, G. and Broughton, W. J. Maximising the use of biological nitrogen fixation in agriculture

This volume contains invited papers given at an FAO/IAEA technicalmeeting held in Rome in March 2001. Most have already been publishedin Plant and Soil 252(1), 2003 and have been reviewed, althoughthe latter is unclear for two papers, those by Cocking and byJensen et al. In that     

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection

Motivation: A plethora of alignment tools have been createdthat are designed to best fit different types of alignment conditions.While some of these are made for aligning Illumina SequenceAnalyzer reads, none of these are fully utilizing its probability(prb) output. In this article, we will introduce a new alignmentapproach (Slider) that reduces the alignment problem space byutilizing each read base's probabilities given in the prb files. Results: Compared with other aligners, Slider has higher alignmentaccuracy and efficiency. In addition, given that Slider matchesbases with probabilities other than the most probable, it significantlyreduces the percentage of base mismatches. The result is thatits SNP predictions are more accurate than other SNP predictionapproaches used today that start from the most probable sequence,including those using base quality. Contact: nmalhis{at}bcgsc.ca Supplementary information and availability: http://www.bcgsc.ca/platform/bioinfo/software/slider Associate Editor: Dmitrij Frishman     

Model-based deconvolution of genome-wide DNA binding

Motivation: Chromatin immunoprecipitation followed by hybridizationto a genomic tiling microarray (ChIP-chip) is a routinely usedprotocol for localizing the genomic targets of DNA-binding proteins.The resolution to which binding sites in this assay can be identifiedis commonly considered to be limited by two factors: (1) theresolution at which the genomic targets are tiled in the microarrayand (2) the large and variable lengths of the immunoprecipitatedDNA fragments. Results: We have developed a generative model of binding sitesin ChIP-chip data and an approach, MeDiChI, for efficientlyand robustly learning that model from diverse data sets. Wehave evaluated MeDiChI's performance using simulated data, aswell as on several diverse ChIP-chip data sets collected onwidely different tiling array platforms for two different organisms(Saccharomyces cerevisiae and Halobacterium salinarium NRC-1).We find that MeDiChI accurately predicts binding locations toa resolution greater than that of the probe spacing, even foroverlapping peaks, and can increase the effective resolutionof tiling array data by a factor of 5x or better. Moreover,the method's performance on simulated data provides insightsinto effectively optimizing the experimental design for increasedbinding site localization accuracy and efficacy. Availability: MeDiChI is available as an open-source R package,including all data, from http://baliga.systemsbiology.net/medichi. Contact: dreiss{at}systemsbiology.org Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop     

Fitting a geometric graph to a protein-protein interaction network

Motivation: Finding a good network null model for protein–proteininteraction (PPI) networks is a fundamental issue. Such a modelwould provide insights into the interplay between network structureand biological function as well as into evolution. Also, network(graph) models are used to guide biological experiments anddiscover new biological features. It has been proposed thatgeometric random graphs are a good model for PPI networks. Ina geometric random graph, nodes correspond to uniformly randomlydistributed points in a metric space and edges (links) existbetween pairs of nodes for which the corresponding points inthe metric space are close enough according to some distancenorm. Computational experiments have revealed close matchesbetween key topological properties of PPI networks and geometricrandom graph models. In this work, we push the comparison furtherby exploiting the fact that the geometric property can be testedfor directly. To this end, we develop an algorithm that takesPPI interaction data and embeds proteins into a low-dimensionalEuclidean space, under the premise that connectivity informationcorresponds to Euclidean proximity, as in geometric-random graphs.We judge the sensitivity and specificity of the fit by computingthe area under the Receiver Operator Characteristic (ROC) curve.The network embedding algorithm is based on multi-dimensionalscaling, with the square root of the path length in a networkplaying the role of the Euclidean distance in the Euclideanspace. The algorithm exploits sparsity for computational efficiency,and requires only a few sparse matrix multiplications, givinga complexity of O(N²) where N is the number of proteins. Results: The algorithm has been verified in the sense that itsuccessfully rediscovers the geometric structure in artificiallyconstructed geometric networks, even when noise is added byre-wiring some links. Applying the algorithm to 19 publiclyavailable PPI networks of various organisms indicated that:(a) geometric effects are present and (b) two-dimensional Euclideanspace is generally as effective as higher dimensional Euclideanspace for explaining the connectivity. Testing on a high-confidenceyeast data set produced a very strong indication of geometricstructure (area under the ROC curve of 0.89), with this networkbeing essentially indistinguishable from a noisy geometric network.Overall, the results add support to the hypothesis that PPInetworks have a geometric structure. Availability: MATLAB code implementing the algorithm is availableupon request. Contact: natasha{at}ics.uci.edu Associate Editor: Olga Troyanskaya     

ELECTROPHORETIC AND MORPHOMETRIC CHARACTERS IN POPULATION DIFERENTIATION OF THE PEARL OYSTER, PINCTADA RADIATA (LEACH), FROM AROUND BAHRAIN

Variation at the leucine aminopeptidase (Lap), glucose phosphateisomerase (Gpi) and tetrazolium oxidase (To) loci was investigatedin samples of three populations, Al-Mayana (MAY), Shigita (SH)and Mina Salman (MS), of Pinctada radiata from pearl oysterbeds around Bahrain. The To locus was monomor-phic. SignificantLap and Gpi heterozygote deficiencies were evident and it issuggested that these were generated by selection. The MS population,to the East of Bahrain, differed significantly in Gpi allelefrequencies from both Northern populations (MAY, SH) and Nei'sgenetic identity indicates a close relationship between theNorthern populations. Measurements of shell morphometrics were used both as ratiosof one dimension to another, and as regressions of one dimensionon another to examine relatedness between populations. Boththese mor-phometric approaches gave different results from eachother and also differed from the electrophoretic data. It isconcluded that estimates of relatedness in pearl oysters basedon electrophoretic data will be more reliable than those basedon shell shape. (Received 20 November 1990; accepted 12 April 1991)     

PETALIFERA HABEI, A NEW SPECIES FROM JAPAN ADDENDUM

Since Petalifera habei was described in the Proceedings, 34,1, 12–18, April 1960, I have received from Dr. K. Babaa short account of the same species in Publ. Seto. mar. biol.Lab. 7, 3, 337–338. December, 1959, under the title "Thegenus Petalifera and a new species, P. ramosa, from Japan".I was unaware that Dr. Baba intended to describe it. As hispaper antedates mine, his name, Petalifera ramosa, must replaceP. Habei.     

Electrophysiological characterization of the node in Chara corallina: functional differentiation for wounding response

Electrical characteristics of the node were analyzed in comparisonwith those of the flank of the internodal cell in Chara corallina.The dependence of the membrane potential of the node on pH andK⁺ concentration was almost the same as that of the flank. Inthe flank, the increase in the Ca²⁺ concentration stopped thedepolarization in the presence of 100 mM KCl. In the node, however,Ca²⁺ could not stop the depolarization induced by 100 mM KCl.It has been reported that the node has a function to tranducethe signal of osmotic shock into a transient depolarization.In combination with osmotic shock, 10 mM K⁺ could induce a long-lastingdepolarization of the node. These electrical characteristicsof the node were suggested to be responsible for the electricalresponse to wounding in Characeae.     

Nuclear Replication Activity During Seed Development, Dormancy Breakage and Germination in Three Tree Species: Norway Maple (Acer platanoidesL.), Sycamore (Acer pseudoplatanusL.) and Cherry (Prunus aviumL.)

Flow cytometric analyses of nuclear DNA levels were carriedout during development, stratification and germination of dormantseeds from three tree species with contrasting characteristics.Norway maple (Acer platanoides) and sycamore (Acer pseudoplatanus)have orthodox (desiccation-tolerant) and recalcitrant (desiccation-sensitive)storage behaviours, respectively, and require only a periodof cold to break dormancy, whereas, orthodox cherry (Prunusavium) seeds require an initial warm period before cold stratificationto fully stimulate germination. Whole embryos and radicle tipsof both Norway maple and sycamore were found to have stablehigh levels of 4C DNA during the latter stages of developmentand both contained nuclei arrested at the 2C and 4C levels atmaturity. Mature cherry embryos had nuclei predominantly arrestedat the 2C level. This suggests that the acquisition of desiccationtolerance is not correlated with the arrest of the cell cycleat any particular nuclear DNA level. Neither DNA replicationin radicle cells nor germination occurred when seeds were maintainedmoist at a constant 20 °C. However, in the late stages ofcold treatment during stratification, nuclear DNA levels inradicle cells changed in advance of radicle emergence in theorthodox Norway maple and cherry, whereas in the recalcitrantsycamore, change was not recorded until after radicle emergence.These results show that DNA replication has potential use asan indicator of the progress of tree seeds through stratificationtreatments used to break some types of dormancy. The ways inwhich this indicator could be exploited for seed quality andperformance testing are discussed.Copyright 1998 Annals of BotanyCompany Norway maple,Acer platanoidesL., sycamore,Acer pseudoplatanusL., cherry,Prunus aviumL., DNA replication, flow cytometry, seed dormancy, stratification     

A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments

Motivation: The proliferation of public data repositories createsa need for meta-analysis methods to efficiently evaluate, integrateand validate related datasets produced by independent groups.A t-based approach has been proposed to integrate effect sizefrom multiple studies by modeling both intra- and between-studyvariation. Recently, a non-parametric ‘rank product’method, which is derived based on biological reasoning of fold-changecriteria, has been applied to directly combine multiple datasetsinto one meta study. Fisher's Inverse ² method, which only dependson P-values from individual analyses of each dataset, has beenused in a couple of medical studies. While these methods addressthe question from different angles, it is not clear how theycompare with each other. Results: We comparatively evaluate the three methods; t-basedhierarchical modeling, rank products and Fisher's Inverse ²test with P-values from either the t-based or the rank productmethod. A simulation study shows that the rank product method,in general, has higher sensitivity and selectivity than thet-based method in both individual and meta-analysis, especiallyin the setting of small sample size and/or large between-studyvariation. Not surprisingly, Fisher's ² method highly dependson the method used in the individual analysis. Application toreal datasets demonstrates that meta-analysis achieves morereliable identification than an individual analysis, and rankproducts are more robust in gene ranking, which leads to a muchhigher reproducibility among independent studies. Though t-basedmeta-analysis greatly improves over the individual analysis,it suffers from a potentially large amount of false positiveswhen P-values serve as threshold. We conclude that careful meta-analysisis a powerful tool for integrating multiple array studies. Contact: fxhong{at}jimmy.harvard.edu Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: David Rocke Present address: Department of Biostatistics and ComputationalBiology, Dana-Farber Cancer Institute, Harvard School of PublicHealth, 44 Binney Street, Boston, MA 02115, USA.     

Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics

Motivation: It has been widely reported that biological networksare robust against perturbations such as mutations. On the contrary,it has also been known that biological networks are often fragileagainst unexpected mutations. There is a growing interest inthese intriguing observations and the underlying design principlethat causes such robust but fragile characteristics of biologicalnetworks. For relatively small networks, a feedback loop hasbeen considered as an important motif for realizing the robustness.It is still, however, not clear how a number of coupled feedbackloops actually affect the robustness of large complex biologicalnetworks. In particular, the relationship between fragilityand feedback loops has not yet been investigated till now. Results: Through extensive computational experiments, we foundthat networks with a larger number of positive feedback loopsand a smaller number of negative feedback loops are likely tobe more robust against perturbations. Moreover, we found thatthe nodes of a robust network subject to perturbations are mostlyinvolved with a smaller number of feedback loops compared withthe other nodes not usually subject to perturbations. This topologicalcharacteristic eventually makes the robust network fragile againstunexpected mutations at the nodes not previously exposed toperturbations. Contact: ckh{at}kaist.ac.kr Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Thomas Lengauer     

Ultrastructure and Secretion of the Secretory Cells of Two Species ofFagoniaL. (Zygophyllaceae)

The ultrastructure and secretion of the secretory cells of theglandular trichomes ofFagonia mollisandF. glutinosawere studied.The most important finding of this study is that two speciesof the same genus produce the lipophilic component of the secretorymaterial in completely different ways and at different siteswithin the cell. In the early stages of development of secretorycells ofF. mollis,numerous mitochondria, containing myelin-likestructures, occur in the basal part of the cell. Above them,highly-elongate elements, which are suspected to develop frommitochondria with myelin-like structures, are present. Thesehave been termed ‘modified mitochondria’. It issuggested that the myelin-like structures are precursors ofthe lipophilic material ofF. mollis.InF. glutinosa,the lipophilicmaterial appears first in the plastids as plastoglobuli. Polysaccharidesappear to be produced by dictyosomes in both species. Secretionof the secretory substance to the outside of the protoplastappears to be granulocrine.Copyright 1998 Annals of Botany Company Fagonia mollis,Fagonia glutinosa,glandular trichomes, secretory cell, mitochondria, modified mitochondria, plastids, dictyosomes, lipophilic material, myelin-like structures, polysaccharides     

EDITORIAL

Science journals face challenges from rapidly evolving businessmodels, diminishing library budgets and an increasing arrayof technological options for delivering content and processingsubmissions through peer review. The Annals of Botany is respondingby continually improving the service it provides to authors,readers and to its subscribers. Accordingly, several enhancementsand further streamlining are planned for 2006. We already makeall our ‘Botanical Briefings’ and ‘InvitedReviews’ available free of charge online from first publication.Annals of Botany now offers all authors the possibility of Open     

3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm

Motivation: Reliable structural modelling of protein–proteincomplexes has widespread application, from drug design to advancingour knowledge of protein interactions and function. This workaddresses three important issues in protein–protein docking:implementing backbone flexibility, incorporating prior indicationsfrom experiment and bioinformatics, and providing public accessvia a server. 3D-Garden (Global And Restrained Docking ExplorationNexus), our benchmarked and server-ready flexible docking system,allows sophisticated programming of surface patches by the uservia a facet representation of the interactors’ molecularsurfaces (generated with the marching cubes algorithm). Flexibilityis implemented as a weighted exhaustive conformer search foreach clashing pair of molecular branches in a set of 5000 modelsfiltered from around 340 000 initially. Results: In a non-global assessment, carried out strictly accordingto the protocols for number of models considered and model qualityof the Critical Assessment of Protein Interactions (CAPRI) experiment,over the widely-used Benchmark 2.0 of 84 complexes, 3D-Gardenidentifies a set of ten models containing an acceptable or bettermodel in 29/45 test cases, including one with large conformationalchange. In 19/45 cases an acceptable or better model is rankedfirst or second out of 340 000 candidates. Availability: http://www.sbg.bio.ic.ac.uk/3dgarden (server) Contact: v.lesk{at}ic.ac.uk Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Burkhard Rost     

A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case

Motivation: The genomic methylation analysis is useful to typebacteria that have a high number of expressed type II methyltransferases.Methyltransferases are usually committed to Restriction andModification (R-M) systems, in which the restriction endonucleaseimposes high pressure on the expression of the cognate methyltransferasethat hinder R-M system loss. Conventional cluster methods donot reflect this tendency. An algorithm was developed for dendrogramconstruction reflecting the propensity for conservation of R-MType II systems. Results: The new algorithm was applied to 52 Helicobacter pyloristrains from different geographical regions and compared withconventional clustering methods. The algorithm works by firstgrouping strains that share a common minimum set of R-M systemsand gradually adds strains according to the number of the R-Msystems acquired. Dendrograms revealed a cluster of Africanstrains, which suggest that R-M systems are present in H.pylorigenome since its human host migrates from Africa. Availability: The software files are available at http://www.ff.ul.pt/paginas/jvitor/Bioinformatics/MCRM_algorithm.zip Contact: filipavale{at}fe.ucp.pt Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop