Protein networks and pathway analysis. Preface

Methods in Molecular Biology (Impact Factor: 1.29). 01/2009; 563:v-vii. DOI: 10.1007/978-1-60761-175-2
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    • "GO enrichment tools are popular (Ashburner et al., 2000; Boyle et al., 2004; Carbon et al., 2009), which look for over-representation of associated GO terms within gene lists. To meet the growing needs of biologists in the omics era, more specialized gene identifier-based search engines have been developed for various model organisms, including free or commercial resources such as functional annotation tools (Huang da et al., 2009), pathway mapping algorithms (Kanehisa and Goto, 2000; Nikolsky and Bryant, 2009; Kelder et al., 2012; Mi et al., 2013; Croft et al., 2014), or protein interaction search tools (Stark et al., 2006). The emergence of central, regularly maintained and updated databases that store genomic variation, ontology, pathway, interaction or phenotypic data has attracted software developers to design 'all-in-one' search engines that enable systematic searches against published, pre-defined gene sets (Subramanian et al., 2005) and/or multiple functional annotation resources (Zhang et al., 2005; Araki et al., 2012). "
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    ABSTRACT: Genome-wide assays and screens typically result in large lists of genes or proteins. Enrichments of functional or other biological properties within such lists can provide valuable insights and testable hypotheses. To systematically detect these enrichments can be challenging and time-consuming, because relevant data to compare against query gene lists are spread over many different sources. We have developed AnGeLi (Analysis of Gene Lists), an intuitive, integrated web-tool for comprehensive and customized interrogation of gene lists from the fission yeast, Schizosaccharomyces pombe. AnGeLi searches for significant enrichments among multiple qualitative and quantitative information sources, including gene and phenotype ontologies, genetic and protein interactions, numerous features of genes, transcripts, translation, and proteins such as copy numbers, chromosomal positions, genetic diversity, RNA polymerase II and ribosome occupancy, localization, conservation, half-lives, domains, and molecular weight among others, as well as diverse sets of genes that are co-regulated or lead to the same phenotypes when mutated. AnGeLi uses robust statistics which can be tailored to specific needs. It also provides the option to upload user-defined gene sets to compare against the query list. Through an integrated data submission form, AnGeLi encourages the community to contribute additional curated gene lists to further increase the usefulness of this resource and to get the most from the ever increasing large-scale experiments. AnGeLi offers a rigorous yet flexible statistical analysis platform for rich insights into functional enrichments and biological context for query gene lists, thus providing a powerful exploratory tool through which S. pombe researchers can uncover fresh perspectives and unexpected connections from genomic data. AnGeLi is freely available at:
    Frontiers in Genetics 11/2015; 6(380). DOI:10.3389/fgene.2015.00330
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    • "For instance, in pathway analysis (Khatri et al., 2012) and gene set enrichment analysis (Subramanian et al., 2005), multiple genes that work together to serve a particular biological function are often analyzed jointly as a gene set. Several pathway repositories, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) (Kanehisa et al., 2004), PANTHER classification system for protein sequence data (Nikolsky and Bryant, 2009), and Reactome pathways in humans (Matthews et al., 2009) have been established, and are continually being updated. For non-Mendelian diseases and complex traits, identification of isolated genetic variants is insufficient to summarize the complex association with disease. "
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    ABSTRACT: Rapid developments in molecular technology have yielded a large amount of high throughput genetic data to understand the mechanism for complex traits. The increase of genetic variants requires hundreds and thousands of statistical tests to be performed simultaneously in analysis, which poses a challenge to control the overall Type I error rate. Combining p-values from multiple hypothesis testing has shown promise for aggregating effects in high-dimensional genetic data analysis. Several p-value combining methods have been developed and applied to genetic data; see Dai et al. (2012b) for a comprehensive review. However, there is a lack of investigations conducted for dependent genetic data, especially for weighted p-value combining methods. Single nucleotide polymorphisms (SNPs) are often correlated due to linkage disequilibrium (LD). Other genetic data, including variants from next generation sequencing, gene expression levels measured by microarray, protein and DNA methylation data, etc. also contain complex correlation structures. Ignoring correlation structures among genetic variants may lead to severe inflation of Type I error rates for omnibus testing of p-values. In this work, we propose modifications to the Lancaster procedure by taking the correlation structure among p-values into account. The weight function in the Lancaster procedure allows meaningful biological information to be incorporated into the statistical analysis, which can increase the power of the statistical testing and/or remove the bias in the process. Extensive empirical assessments demonstrate that the modified Lancaster procedure largely reduces the Type I error rates due to correlation among p-values, and retains considerable power to detect signals among p-values. We applied our method to reassess published renal transplant data, and identified a novel association between B cell pathways and allograft tolerance.
    Frontiers in Genetics 02/2014; 5:32. DOI:10.3389/fgene.2014.00032
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    ABSTRACT: Gene expression signatures of toxicity and clinical response benefit both safety assessment and clinical practice; however, difficulties in connecting signature genes with the predicted end points have limited their application. The Microarray Quality Control Consortium II (MAQCII) project generated 262 signatures for ten clinical and three toxicological end points from six gene expression data sets, an unprecedented collection of diverse signatures that has permitted a wide-ranging analysis on the nature of such predictive models. A comprehensive analysis of the genes of these signatures and their nonredundant unions using ontology enrichment, biological network building and interactome connectivity analyses demonstrated the link between gene signatures and the biological basis of their predictive power. Different signatures for a given end point were more similar at the level of biological properties and transcriptional control than at the gene level. Signatures tended to be enriched in function and pathway in an end point and model-specific manner, and showed a topological bias for incoming interactions. Importantly, the level of biological similarity between different signatures for a given end point correlated positively with the accuracy of the signature predictions. These findings will aid the understanding, and application of predictive genomic signatures, and support their broader application in predictive medicine.
    The Pharmacogenomics Journal 08/2010; 10(4):310-23. DOI:10.1038/tpj.2010.35 · 4.23 Impact Factor
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