1,721,203 research outputs found
Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration
No full textPattern recognition in gene expression profiling using cDNA microarray: a comparative study of different statistical methods applied to cancer classification
No full textProbability of conception on different days of the menstrual cycle: an ongoing exercise
No full textThe design of the European Multicenter Study on the probabilities of conception in different days of the menstrual cycle is reviewed. Some results, based on part of the data, are presented. These can be summarized as follows: a) Estimates of the probabilities of conception are lower than the ones previously reported in the literature; b) A strong effect of the man's age on fecundability was found. No evidence of a similar impact of the woman's age was demonstrated; c) The number of days with 'most fertile' mucus and parity affect fecundability
Statistical Tools for Gene Expression Analysis and Systems Biology and Related Web Resources
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Effect of normalizations on detecting differentially expressed genes with cDNA microarray experiments.
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Similarity Measures Based on the Overlap of Ranked Genes Are Effective for Comparison and Classification of Microarray Data
No full textSimilarity (or conversely distance) measures are at the heart of most bioinformatic applications. When the similarity involves only a small subset of features out of many, global similarity measures may be significantly affected by noise. Selecting only a subset of (putatively relevant) features for comparison is a widespread solution to the problem albeit affected by arbitrariness and manual intervention. The problem is becoming more and more important due to the increasing amount of experimental data available. In recent years measures based on ranking similarities between two datasets have been proposed. Here, we use one of the proposed rank similarity measures, sharing some aspects with the fraction enrichment score used for protein structure prediction and the gene set enrichment analysis, and test its performance in classifying experiments.
The discrimination ability of the similarity measures based on the overlap of ranked genes tested here compares well or better with standard measures of similarity. This conclusion supports the use of rank-based proximity measures to gain further insight in dataset comparisons, particularly on expression data obtained by different techonologies (e.g., RNA-seq and microarrays)
Gene flow and genetic diversity: a comparison of freshwater bryozoan populations in Europe and North America
No full textWe have used microsatellite and mitochondrial sequence data to gain insight into patterns of gene flow and genetic diversity among North American and European populations of the freshwater bryozoan Cristatella mucedo. Mitochondrial sequence data reveal numerous, widely distributed, divergent genetic lineages in North America that can be broadly categorized into two groups, one of which is genetically homogeneous and relatively similar to the European haplotypes, the other of which is more diverse. The maximum North American sequence differentiation translates into a divergence time of approximately 1.5 Myr BP. In contrast, European populations contained only three haplotypes that are all closely related. Microsatellite data reveal higher overall levels of genetic diversity in North America than Europe, although levels of within-population genetic variation are similar on the two continents. In North America, two of the three microsatellite loci show bimodal distributions of allele sizes which are significantly associated between the two loci. As a result, two microsatellite lineages are evident, and these are assortatively distributed between the mitochondrial haplotype groupings. The combined mitochondrial and microsatellite data suggest two distinct genetic lineages in North America that may represent cryptic species. Hybridization between the two presumptive species or subspecies may have contributed to the high levels of genetic diversity in North America. The overall lower levels of genetic diversity in Europe can be attributed to postglacial derivation of extant populations from a single mitochondrial lineage, and conformation to a metapopulation structure
Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests
No full textThe comparison of several statistical methods currently used for detection of differentially expressed genes was attempted both by a simulation approach and by the analysis of data sets of human expressed sequence tags, obtained from UniGene. In the simulated mixed case, mimicking a situation close to reality, the general chi(2) test was unexpectedly the most efficient in multiple tag sampling experiments, especially when dealing with variations affecting weakly expressed genes. On the other hand, Audic and Claverie's method proved the most efficient for detecting differences in gene expression when dealing with pairwise comparisons. By applying the above methods on UniGene-based data sets concerning two human kidney tumours compared with normal kidney tissue, three novel genes overexpressed in these tumours were identified. Software and additional information on statistical methodologies, simulation approach and data are available at http://telethon.bio.unipd.it/bioinfo/IDEG6/
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