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.     

BicOverlapper: a tool for bicluster visualization

Summary: BicOverlapper is a tool to visualize biclusters fromgene-expression matrices in a way that helps to compare biclusteringmethods, to unravel trends and to highlight relevant genes andconditions. A visual approach can complement biological andstatistical analysis and reduce the time spent by specialistsinterpreting the results of biclustering algorithms. The techniqueis based on a force-directed graph where biclusters are representedas flexible overlapped groups of genes and conditions. Availability: The BicOverlapper software and supplementary materialare available at http://vis.usal.es/bicoverlapper Contact: rodri{at}usal.es Associate Editor: John Quackenbush The first two authors should be reported as joint first authors.     

Power enhancement via multivariate outlier testing with gene expression arrays

Motivation: As the use of microarrays in human studies continuesto increase, stringent quality assurance is necessary to ensureaccurate experimental interpretation. We present a formal approachfor microarray quality assessment that is based on dimensionreduction of established measures of signal and noise componentsof expression followed by parametric multivariate outlier testing. Results: We applied our approach to several data resources.First, as a negative control, we found that the Affymetrix andIllumina contributions to MAQC data were free from outliersat a nominal outlier flagging rate of =0.01. Second, we createda tunable framework for artificially corrupting intensity datafrom the Affymetrix Latin Square spike-in experiment to allowinvestigation of sensitivity and specificity of quality assurance(QA) criteria. Third, we applied the procedure to 507 Affymetrixmicroarray GeneChips processed with RNA from human peripheralblood samples. We show that exclusion of arrays by this approachsubstantially increases inferential power, or the ability todetect differential expression, in large clinical studies. Availability: http://bioconductor.org/packages/2.3/bioc/html/arrayMvout.htmland http://bioconductor.org/packages/2.3/bioc/html/affyContam.htmlaffyContam (credentials: readonly/readonly) Contact: aasare{at}immunetolerance.org; stvjc{at}channing.harvard.edu The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors. Associate Editor: Trey Ideker     

Isolation of Subunits of Coupling Factor 1 from Maize and Spinach Chloroplasts and Properties of Combinations of Subunits with ATPase Activity

Subunits (, ß, ) and mixtures of subunits ( ß, , ß , ß ) were isolated without denaturationfrom a chloroform extract of chloroplast coupling factor 1 (CF₁)from maize (Zea mays var. Ushiku 5-4) and from spinach by fastprotein liquid chromatography (FPLC), on an anion-exchange columnof Mono-Q in the presence of n-octylglucoside (OG) and on achromatofocusing column of Mono-P. The ß -subunitcomplex (CF¹ ß ) was the minimum unit required forATPase activity, as was confirmed by the reconstituted complexof ß and subunits. An subunit isolated from maizeinhibited the ATPase activity of CF₁ ß from bothmaize and spinach. CF₁ ß was found to contain anOG-dependent Mg²⁺-ATPase. The ATPase activity of CF₁ ß required divalent cations, such as Mg²⁺ or Mn²⁺, for its expressionin the presence of OG; its optimum pH was 8.0 and it was markedlyinhibited by NaN₃. The enzyme hydrolyzed ATP in prefernece toGTP but not CTP, UTP, ADP, AMP or pNPP. Lineweaver-Burk plotsof its activity were curvilinear in the range of 0.6–0.7mM ATP.Mg²⁺. ¹Present address: Department of Biology, School of Education,Waseda University, Shinjuku-ku, Tokyo, 160 Japan. (Received February 15, 1989; Accepted April 20, 1989)     

Thermodynamic Roles of Solubility in Taste Responses of Amino Acids

Bitter, sour and sweet responses of amino acids were relatedto their solubilities S_w, which are virtually equal to the reciprocalsof activity coefficients at infinite dilution in water _w, andalso related to their excess partial molar entropies of transferTS_t^E. Chem. Senses 21: 405–409, 1996. Present address: 5-32-12 Tamanawa, Kamakura-shi, 247 Japan     

Discovery of Natural Photosynthesis using Zn-Containing Bacteriochlorophyll in an Aerobic Bacterium Acidiphilium rubrum

We discovered natural photosynthesis using Zn-containing bacteriochlorophyll in an acidophilic bacterium Acidiphilium rubrum. Chemical analysisof the cell extracts gave a 13 : 2 :1 molar ratio of Zn-bacteriochlorophyll : Mg-bacteriochlorophyll : bacteriopheophytin . Most of thepigments are associated with fully active reaction center andlight-harvesting complexes analogous to those in purple photosyntheticbacteria. The finding indicates an unexpectedly wide variabilityof photosynthesis. ⁷Present address: Department of Ecological Engineering, ToyohashiUniversity of Technology, Tenpaku-cho, Toyohashi, 441 Japan     

From pull-down data to protein interaction networks and complexes with biological relevance

Motivation: Recent improvements in high-throughput Mass Spectrometry(MS) technology have expedited genome-wide discovery of protein–proteininteractions by providing a capability of detecting proteincomplexes in a physiological setting. Computational inferenceof protein interaction networks and protein complexes from MSdata are challenging. Advances are required in developing robustand seamlessly integrated procedures for assessment of protein–proteininteraction affinities, mathematical representation of proteininteraction networks, discovery of protein complexes and evaluationof their biological relevance. Results: A multi-step but easy-to-follow framework for identifyingprotein complexes from MS pull-down data is introduced. It assessesinteraction affinity between two proteins based on similarityof their co-purification patterns derived from MS data. It constructsa protein interaction network by adopting a knowledge-guidedthreshold selection method. Based on the network, it identifiesprotein complexes and infers their core components using a graph-theoreticalapproach. It deploys a statistical evaluation procedure to assessbiological relevance of each found complex. On Saccharomycescerevisiae pull-down data, the framework outperformed othermore complicated schemes by at least 10% in F₁-measure and identified610 protein complexes with high-functional homogeneity basedon the enrichment in Gene Ontology (GO) annotation. Manual examinationof the complexes brought forward the hypotheses on cause offalse identifications. Namely, co-purification of differentprotein complexes as mediated by a common non-protein molecule,such as DNA, might be a source of false positives. Protein identificationbias in pull-down technology, such as the hydrophilic bias couldresult in false negatives. Contact: samatovan{at}ornl.gov Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Jonathan Wren Present address: Department of Biomedical Informatics, VanderbiltUniversity, Nashville, TN 37232. The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors.     

LibSBML: an API library for SBML

Summary: LibSBML is an application programming interface libraryfor reading, writing, manipulating and validating content expressedin the Systems Biology Markup Language (SBML) format. It iswritten in ISO C and C++, provides language bindings for CommonLisp, Java, Python, Perl, MATLAB and Octave, and includes manyfeatures that facilitate adoption and use of both SBML and thelibrary. Developers can embed libSBML in their applications,saving themselves the work of implementing their own SBML parsing,manipulation and validation software. Availability: LibSBML 3 was released in August 2007. Sourcecode, binaries and documentation are freely available underLGPL open-source terms from http://sbml.org/software/libsbml. Contact: sbml-team{at}caltech.edu Associate Editor: Olga Troyanskaya The first two authors should be regarded as First Author.     

Part of the Lysyl Residues in Wheat {alpha}-Amylase is Methylated as N-{varepsilon}-Trimethyl Lysine

Amino acid analyses of wheat -amylase purified from germinatingseeds by affinity chromatography showed a high content of amodified lysyl residue. The modified residue was identifiedas N--trimethyl lysine. The presence of trimethyl lysine in-amylase is discussed in terms of isozymes. ¹ Present address: National Institutes of Health, Bldg. 10,Rm. 9B-15, Bethesda, MD 20205, U.S.A. (Received August 20, 1981; Accepted March 19, 1982)     

Regulation of sexual agglutinability in Saccharomyces cerevisiae of {alpha} and {alpha} types by sex-specific factors produced by their respective opposite mating types

The sexual agglutinability of haploid cells of heterothallicSaccharomyces cerevisiae was repressed when they were culturedin the absence of easily fermentable sugars, such as glucoseand mannose. The repression was reversed by the action of hormone-likesubstances of the opposite mating types. The substance producedby mating type cells was identical to subtsance-I which isknown to induce sexual agglutinability of inducible matingtype cells. The mating type cells produce a new hormone-likesubstance which induces or enhances sexual agglutinability of mating type cells. A crude fraction of the mating type-specific substance ( substance-I)was obtained by passing the culture filtrate of mating typecells through Amberlite CG-50 (H⁺ form), followed by elutionwith 1.5 M ammonia. ² On leave from Osaka City University. (Received December 25, 1975; )     

Metabolic conversion of N-methyl carbon of {gamma}-glutamylmethylamide to caffeine in tea plants

Tea seedlings were treated with ¹⁴C-methylamine to cause synthesisof ¹⁴C--glutamylmethylamide (N-methyl-¹⁴C). The metabolic conversionof -glutamylmethylamide was studied by tracing ¹⁴C. ¹⁴C--Glutamylmethylamide (N-methyl-¹⁴C) translocated from rootsand cotyledons to shoots of tea seedlings, was converted almostentirely into caffeine. Conversion was greater in light-exposedsamples. For those grown in the dark, the converted amount didnot correspond to the total caffeine produced. More ¹⁴C--glutamylmethylamidewas present in stems than in leaves, but with ¹⁴C-caffeine,the opposite was found. When ¹⁴C--glutamylmethylamide or ¹⁴C-methylamine was appliedto leaf disks, ¹⁴C-caffeine was biosynthesized from both substances. ¹ Present address: Department of Agricultural Chemistry, ShizuokaUniversity, Iwata, Shizuoka 438, Japan. (Received September 25, 1971; )     

Characterization of the mRNA for the {alpha}-Amylase from Wheat

Characterization of the mRNA for the -amylase from wheat wasmade by fractionation of the total membrane-bound polysomalRNA and by immunoprecipitation of in vitro synthesized -amylaseby its specific antibody. The content of the mRNA for the -amylasein the membrane-bound polysomal fraction from germinating wheatseeds was estimated as 5–10% of the total mRNA in thisfraction. RNA, separated in high resolution on acid-urea-agarosegels by electrophoresis, was recovered from the gels by a newmethod. Its translation products in rabbit reticulocyte lysateswere analyzed with a specific antibody against -amylase. Thesize of the mRNA for -amylase was estimated as 5.0?10⁵ daltons. ¹ Present address: National Institutes of Health, Bldg. 10,Rm. 9B-15, Bethesda, MD 20205, U.S.A. (Received March 6, 1982; Accepted August 4, 1982)     

In Vitro Translation of {alpha}-Amylase mRNA from Dry Wheat Embryos

The poly(A)⁺RNA fraction was separated from ungerminated wheatembryos and translated in both wheat germ extract and rabbitreticulocyte lysate systems. The polypeptides synthesized invitro were immunoprecipitated using rabbit anti-wheat -amylaseantibody. Fluorography after SDS-polyacrylamide gel electrophoresisshowed a band of molecular weight of 43,000, which was the sameas that of the -amylase precursor polypeptide. The -amylaseprecursor synthesized from the mRNA of dry embryos belongedto the group II isozyme subset, characterized by an acidic isoelectricpoint. ²Present address: Matsumae High SchoolMatsumae-cho, Hokkaido049-15, Japan. (Received February 1, 1988; Accepted June 1, 1988)     

Natural Abundance of {delta}15N Confirms Insectivorous Habit ofRoridula gorgonias, Despite it Having No Proteolytic Enzymes

Natural abundance values of plant ¹⁵N give an indication asto the source of nitrogen. In particular, carnivorous plantsare expected to be relatively enriched due to trophic enrichmentof their prey. Values of ¹⁵N for adultRoridula gorgonias(mean+3.02)are 4–9 greater than co-occurring non-carnivorous plantspecies and 5.24 greater than juvenileR. gorgoniasplants. Theyare also 3.5–4.26 greater than co-occurringDroseraspecieswhich, being sundews, are considered to be carnivorous. Thesehigh levels of ¹⁵N in adult plants are best explained as beingdue to access to trophically enriched N from insects. As isthe case for other carnivorous plants, leaves and stems ofR.gorgoniasare highly ultraviolet reflective and are thereforeprobably attractive to potential insect prey. This is furthersupport for this plant species being insectivorous.Copyright1998 Annals of Botany Company Nitrogen isotopes, carnivorous plants, insectivorous plant, ultraviolet,Roridula gorgoniasL.     

Variation in Natural Abundance of 15N among Plant Parts and in 15N/14N Fractionation during N2 Fixation in the Legume-Rhizobia Symbiotic System

Sixteen legumes were grown in N-free media so that N was suppliedentirely by symbiotic N₂ fixation. The plant tissues were analyzedfor natural ¹⁵N abundance (expressed as ¹⁵N per mil relativeto air N₂) with a ratio mass spectrometer. The nodules of desmodium,centro, siratro, soybean and winged bean showed high enrichmentin ¹⁵N (+9), while red clover showed slight enrichment (+2).The nodules of 9 other forage legumes (Townsville stylo, whiteclover, alsike clover, common vetch, Chinese milk vetch, senna,alfalfa, ladino clover, and hairy vetch) showed little enrichmentin ¹⁵N. In all the legumes investigated, particularly in the ureide-transportingplants such as desmodium, centro, siratro, soybean, winged beanand field bean, the ¹⁵N value of the shoots was negative (–3.2).The ¹⁵N value of the shoots in winged bean and field bean variedby about 1 depending on the Rhizobium strains used. The isotopicmass balance of 13 legumes indicated that isotopic fractionationoccurs during N₂ fixation by the legume-rhizobia symbiosis witha preference for ¹⁴N over ¹⁵N, resulting in a ¹⁵N value of –0.2to –2 in the whole plant. The results indicate that ¹⁵N/¹⁴N isotopic discrimination witha preference for the lighter atom may occur in both N₂ fixationand export of fixed N from nodules. ¹Present address: Department of Soils and Fertilizers, NationalAgriculture Research Center, Kannondai, Tsukuba, Ibaraki 305,Japan. (Received October 8, 1985; Accepted April 7, 1986)     

Alternative Methods of Analysing Water Potential Isotherms: Some Cautions and Clarifications: I. THE IMPACT OF NON-IDEALITY AND OF SOME EXPERIMENTAL ERRORS

In recent years alternative ways have been proposed to transformmeasurements of leaf water potential, , and relative water content,R^*, in order to derive values of osmotic pressure at full turgidityin leaves and shoots, ^o(when 0). Two types of transformationsare usually considered: 1/ versus R^* and versus 1/R^*, and linearregression is used to fit the data in the region where turgoris thought to be zero. It appears that when ^o is estimated bylinear extrapolation of 1/Psi; versus R^* then apoplastic watermight not influence the accuracy of ^o but when the versus \/R^*transformation is used apoplastic water causes an underestimateof ^o. We examine the accuracy of the estimate of ^o obtainedfrom the two transformations when there are random errors in, systematic errors in , and when the osmotic solutions arenon-ideal. The 1/ versus R^* transformation generally producesthe best estimate of ⁰ by linear extrapolation.     

Adaptation of the Euryhaline Charophyte Lamprothamnium papulosum to Brackish and Freshwater: Turgor Pressure and Vacuolar Solute Concentrations During Steady-State Culture and After Hypo-osmotic Treatment

The euryhaline charophyte Lamprothamnium papulosum (Wallr.)J. Gr. was adapted to media with decreasing salinities rangingfrom 550 to 0 mosmol kg^–1. Vegetative plants grown inmedia with osmotic pressures (⁰) in the range of 550 to 130mosmol kg^–1 maintained a constant turgor pressure () at309 + 7 mosmol kg^–1. The ions K+, Na+ and Cl–, werethe predominant solutes in the vacuole. Changes in their concentrationsaccount for the variation in internal osmotic pressure (¹) with,⁰. The divalent ions Mg²⁺, Ca²⁺ and were also present in significant amounts, but their concentrationsdid not alter with changes in, ⁰. In cells subjected to hypo-osmotic shock the regulation of was incomplete. The turgor pressure increased from 302 to 383mosmol kg^–1. The first rapid response to the sudden decreasein ⁰ was a loss of K⁺ and Cl^–. In contrast to the decreasein ionic concentrations an accumulation of sucrose occurredwhich could account for the increase of . The increase in sucroseconcentration started 24 to 48 h after the downshock and reachedits highest value after 3 to 4 weeks. The sucrose concentrationin the vacuole was up to 320 mol m^–3. During this timethe ionic content continued to decrease but did not counterbalancethe sucrose concentration sufficiently to regain the original. High sucrose levels accompanied by an enhanced were also observedduring the period of fructification (sexual reproduction: formationof antheridia and oogonia) in Lamprothamnium kept under conditionsof constant salinity. It is concluded that high sucrose content and elevated arecharacteristic of sexual reproduction in this charophyte. Lamprothamniumis able to tolerate different during various developmentalstages (e.g. vegetative and reproductive phases). Key words: Lamprothamnium papulosum, sucrose, turgor pressure     

A Rapid and Sensitive Method for Determination of Relative Specificity of RuBisCO from Various Species by Anion-Exchange Chromatography

A rapid and sensitive method to determine the relative specificity() of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO)using anion-exchange chromatography is described. We employedthe open gas system for the reaction of RuBisCO to get the mostreliable CO₂ and O₂ concentrations in the reaction mixture.3-Phosphoglycerate and 2-phosphoglycolate which were formedin the RuBisCO reaction were completely separated and directlymeasured with anion-exchange chromatography without using radioisotopes.The determination of the value was accomplished in 3 h. The values of RuBisCO enzymes from higher land plants were between90 and 96, and those from bacteria including cyanobacteriumwere close to 45. These values were in agreement with previouslyreported values. The enzyme of the red macroalga Porphyra yezoensisexhibited a value of over 140, as expected from the reportedvalue of the enzyme from the red microalga Porphyridium cruenteum.RuBisCO from the green macroalga Ulva pertusa had a value closeto 70 and similar to that of the enzyme from the green microalgaChlamydomonas reinhardtii. ⁴On leave from Research and Development Center, Unitika Ltd.,23 Kozakura, Uji, Kyoto, 611 Japan. ⁵Present address: Nara Institute of Science and Technology,8916-5 Takayama-Cho, Ikoma, Nara, 630-01 Japan