Investigating the effect of paralogs on microarray gene-set analysis

Background  

In order to interpret the results obtained from a microarray experiment, researchers often shift focus from analysis of individual differentially expressed genes to analyses of sets of genes. These gene-set analysis (GSA) methods use previously accumulated biological knowledge to group genes into sets and then aim to rank these gene sets in a way that reflects their relative importance in the experimental situation in question. We suspect that the presence of paralogs affects the ability of GSA methods to accurately identify the most important sets of genes for subsequent research.     

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

ABSTRACT: BACKGROUND: Gene-set enrichment analyses (GEA or GSEA) are commonly used for biological characterization of an experimental gene-set. This is done by finding known functional categories, such as pathways or Gene Ontology terms, that are over-represented in the experimental set; the assessment is based on an overlap statistic. Rich biological information in terms of gene interaction network is now widely available, but this topological information is not used by GEA, so there is a need for methods that exploit this type of information in high-throughput data analysis. RESULTS: We developed a method of network enrichment analysis (NEA) that extends the overlap statistic in GEA to network links between genes in the experimental set and those in the functional categories. For the crucial step in statistical inference, we developed a fast network randomization algorithm in order to obtain the distribution of any network statistic under the null hypothesis of no association between an experimental gene-set and a functional category. We illustrate the NEA method using gene and protein expression data from a lung cancer study. CONCLUSIONS: The results indicate that the NEA method is more powerful than the traditional GEA, primarily because the relationships between gene sets were more strongly captured by network connectivity rather than by simple overlaps.     

Comparative analysis of coiled-coil prediction methods

In this study we compare commonly used coiled-coil prediction methods against a database derived from proteins of known structure. We find that the two older programs COILS and PairCoil/MultiCoil are significantly outperformed by two recent developments: Marcoil, a program built on hidden Markov models, and PCOILS, a new COILS version that uses profiles as inputs; and to a lesser extent by a PairCoil update, PairCoil2. Overall Marcoil provides a slightly better performance over the reference database than PCOILS and is considerably faster, but it is sensitive to highly charged false positives, whereas the weighting option of PCOILS allows the identification of such sequences.     

Comparative evaluation of microarray analysis software

A wide variety of software tools are available to analyze microarray data. To identify the optimum software for any project, it is essential to define specific and essential criteria on which to evaluate the advantages of the key features. In this review we describe the results of our comparison of several software tools. We then conclude with a discussion of the subset of tools that are most commonly used and describe the features that would constitute the “ideal microarray analysis software suite.”     

Comparative evaluation of different preservation methods for cyanobacterial strains

Maintaining pure cultures using preservation methods is of high importance for biotechnological purposes. However, preservation does not necessarily guarantee the genetic stability of these cultures. Therefore, preservation methods are currently needed to assure viability as well as genetic, physiological, and morphological integrity across storage periods. In this study, preservation of five isolates from the microalgae and cyanobacteria collection of the Plant Biology Department, Federal University of Viçosa, Minas Gerais, Brazil was investigated via monthly analyses of cell viability, biomass recovery, and contaminant concentrations over a period of 120 days. Lyophilization was adequate for both heterocystous cyanobacteria and other strains that were able to differentiate hormogones or to synthesize thick layers of exopolysaccharides. Lyophilization was also able to maintain cultures with low levels of contaminants. Dimethyl sulfoxide was relatively efficient, though some of the strains were susceptible to its cytotoxic effects. Our results demonstrated that cryopreservation with glycerol was the most efficient method. The ability to routinely preserve cyanobacterial strains reduces costs associated with maintaining large culture collections and reduces the risks of losing particular strains or species through contamination and genetic drift. The results obtained in this study are therefore discussed in the context of the efficiency of the methods and the current need to develop suitable methods for maintenance of cyanobacterial collections.     

Comparative evaluation of methods for detecting HBsAg in sera

The results of the analysis of 1209 serum samples, made with a view to detecting those containing HBsAg, are presented. This analysis was made by the radioimmunoassay (RIA) on a polyethylene film, by the standard RIA technique with the use of a diagnostic kit obtained from Abbott Laboratories (USA) and by the passive hemagglutination (PHA) test. The RIA film technique was found to have the sensitivity of about 2 ng/ml HBsAg, which is similar to the sensitivity of the kit from Abbott Laboratories and exceeds the sensitivity of the PHA test approximately 50-fold. The percentage of detected HBsAg-positive sera, yielded by analysis with the use of the RIA film technique and the standard RIA technique, is the same. The RIA technique make it possible to detect more positive sera than the PHA test by about 2.5%.     

Comparative evaluation of the methods of determining perfringens A antitoxin

The methods for determining the level of type A Perfringens antitoxin in human blood sera were examined and compared. The ratios for correlating the data obtained in the toxin neutralization test (NT) in vivo, in the passive hemagglutination test (PHT), and as a result of the enzyme-labeled immunosorbent assay (ELISA) with regard to the antitoxin level measured in the NT in vitro were equal to 0.88, 0.64 and 0.39, respectively. The sensitivity of the NT in vivo and in vitro was 0.25 IU/ml, that of the PHT 0.01-0.005 IU/ml, and that of the ELISA 0.01-0.02 IU/ml Perfringens antitoxin. To perform the NT, not less than 1 ml blood serum is required, while for the PHT and ELISA, 0.1-0.05 ml. Provided hyghly purified anatoxin is used for preparing the erythrocyte diagnosticum Perfringens, and polysterene plates are sensitized in performing the ELISA, all the reactions are specific. While titrating human blood sera containing type A Perfringens antitoxin, use in the PHT may be made of type A Perfringens rabbit antiserum as reference.     

Comparative evaluation of spin-label modeling methods for protein structural studies

Site-directed spin-labeling electron paramagnetic resonance spectroscopy is a powerful technique for the investigation of protein structure and dynamics. Accurate spin-label modeling methods are essential to make full quantitative use of site-directed spin-labeling electron paramagnetic resonance data for protein modeling and model validation. Using a set of double electron-electron resonance data from seven different site pairs on maltodextrin/maltose-binding protein under two different conditions using five different spin labels, we compare the ability of two widely used spin-label modeling methods, based on accessible volume sampling and rotamer libraries, to predict experimental distance distributions. We present a spin-label modeling approach inspired by canonical side-chain modeling methods and compare modeling accuracy with the established methods.     

不同粪便DNA提取方法比较分析北大核心CSCD

肠道微生物群落结构和多样性与人体疾病密切相关。然而,相关群落结构分析结果可能受到DNA提取质量等实验因素影响。因此,评估不同DNA提取方法对肠道特定种属的提取效果,对于全面、准确获取人体肠道微生物谱,深入探究肠道微生物群落结构具有指导意义。本研究旨在借助实时荧光定量PCR(real-time quantitative polymerase chain reaction,RT qPCR)技术,以DNA提取纯度、浓度,以及对肠道中特定种属微生物基因组DNA的提取丰度为指标,对5种DNA提取方法进行比较分析。结果表明,试剂盒Q的提取效果最佳,特别是对乳杆菌属和双歧杆菌属等革兰氏阳性菌的提取效果较好。N试剂盒的平均DNA提取浓度较Q试剂盒低,但在纯度方面,二者无显著性差异。与其他3种商用试剂盒(M、PSP、TG)相比,N方法对肠道内指定微生物基因组的提取效果仅次于Q试剂盒,位居第二。相比之下,M试剂盒提取所得DNA,质量较高,但浓度偏低,对于肠道内革兰氏阳性菌的提取效果不很理想。TG试剂盒和PSP试剂盒提取所得DNA在浓度、质量以及细菌丰度方面均不及其他验证的试剂盒。综上,Q试剂盒可作为肠道微生态研究相关实验中获取高质量基因组DNA的提取方法。本研究结果为肠道微生态研究相关实验中基因组DNA提取方法的选择提供参考依据。     

Kiwi: a tool for integration and visualization of network topology and gene-set analysis

Background

The analysis of high-throughput data in biology is aided by integrative approaches such as gene-set analysis. Gene-sets can represent well-defined biological entities (e.g. metabolites) that interact in networks (e.g. metabolic networks), to exert their function within the cell. Data interpretation can benefit from incorporating the underlying network, but there are currently no optimal methods that link gene-set analysis and network structures.

Results

Here we present Kiwi, a new tool that processes output data from gene-set analysis and integrates them with a network structure such that the inherent connectivity between gene-sets, i.e. not simply the gene overlap, becomes apparent. In two case studies, we demonstrate that standard gene-set analysis points at metabolites regulated in the interrogated condition. Nevertheless, only the integration of the interactions between these metabolites provides an extra layer of information that highlights how they are tightly connected in the metabolic network.

Conclusions

Kiwi is a tool that enhances interpretability of high-throughput data. It allows the users not only to discover a list of significant entities or processes as in gene-set analysis, but also to visualize whether these entities or processes are isolated or connected by means of their biological interaction. Kiwi is available as a Python package at http://www.sysbio.se/kiwi and an online tool in the BioMet Toolbox at http://www.biomet-toolbox.org.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0408-9) contains supplementary material, which is available to authorized users.     

两种方法诊断女性需氧菌阴道炎的对比分析

摘要：目的 对比分析两种方法诊断女性需氧菌阴道炎的效果。方法 使用Donders湿片高倍镜检法、Tempera临床和微生物诊断法对2014年5月至2015年4月妇科门诊8 326例就诊患者需氧菌感染情况进行对比分析。结果 在8 326例就诊患者中,采用Donders湿片高倍镜检法检出需氧菌阴道炎患者1 819例,检出率为21.8%;采用Tempera临床和微生物诊断法检出需氧菌阴道炎患者1 825例,检出率为21.9%。通过SPSS13.0统计学分析,两种方法在需氧菌阴道炎检出率方面不存在显著差异（χ2=20.4,P>0.05）。结论 这两种方法诊断需氧菌阴道炎具有很好的一致性,医院可根据自身实际情况选择其中一种。南宁地区女性需氧菌阴道炎检出率仅次于细菌性阴道病,针对需氧菌阴道炎应采取科学有效的治疗方案,提升需氧菌阴道炎治疗效率。     

两种方法诊断女性需氧菌阴道炎的对比分析

目的对比分析两种方法诊断女性需氧菌阴道炎的效果。方法使用Donders湿片高倍镜检法、Tempera临床和微生物诊断法对2014年5月至2015年4月妇科门诊8 326例就诊患者需氧菌感染情况进行对比分析。结果在8 326例就诊患者中,采用Donders湿片高倍镜检法检出需氧菌阴道炎患者1 819例,检出率为21.8%;采用Tempera临床和微生物诊断法检出需氧菌阴道炎患者1 825例,检出率为21.9%。通过SPSS13.0统计学分析,两种方法在需氧菌阴道炎检出率方面不存在显著差异(χ2=20.4,P0.05)。结论这两种方法诊断需氧菌阴道炎具有很好的一致性,医院可根据自身实际情况选择其中一种。南宁地区女性需氧菌阴道炎检出率仅次于细菌性阴道病,针对需氧菌阴道炎应采取科学有效的治疗方案,提升需氧菌阴道炎治疗效率。