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Complex cellular processes are modular and are accomplished by the concerted action of functional modules (Ravasz et al., Science 2002;297:1551-1555; Hartwell et al., Nature 1999;402:C47-52). These modules encompass groups of genes or proteins involved in common elementary biological functions. One important and largely unsolved goal of functional genomics(More)
The Gene Ontology and annotations derived from the S. cerivisiae Genome Database were analyzed to calculate functional similarity of gene products. Three methods for measuring similarity (including a distance-based approach) were implemented. Significant, quantitative relationships between similarity and expression correlation of pairs of genes were(More)
Motivation: Bio-ontologies, such as the Gene Ontology, represent important sources of prior knowledge that may be automatically integrated to support predictive data analysis tasks. The assessment of similarity of gene products provides the basis for the implementation of classification tools and the automated validation of functional associations. This(More)
1 Superconvergent discontinuous Galerkin methods for second-order elliptic problems / A multiscale finite element method for partial differential equations posed in domains with rough boundaries / Alexandre L. Madureira 35 Convergence and optimality of adaptive mixed finite element methods / 79 Overlapping additive Schwarz preconditioners for elliptic PDEs(More)
The Gene Ontology (GO) is an important knowledge resource for biologists and bioinformaticians. This paper explores the integration of similarity information derived from GO into clustering-based gene expression analysis. A system that integrates GO annotations, similarity patterns and expression data in yeast is assessed. In comparison with a clustering(More)
BACKGROUND Genomics and proteomics analyses regularly involve the simultaneous test of hundreds of hypotheses, either on numerical or categorical data. To correct for the occurrence of false positives, validation tests based on multiple testing correction, such as Bonferroni and Benjamini and Hochberg, and re-sampling, such as permutation tests, are(More)
There is a need to develop methods to automatically incorporate prior knowledge to support the prediction and validation of novel functional associations. One such important source is represented by the Gene Ontology (GO)(™) and the many model organism databases of gene products annotated to the GO. We investigated quantitative relationships between the(More)
To the Editor: Pulmonary nontuberculous mycobacteria (NTM) diseases share clinical signs with tuberculosis (TB), causing a clinical dilemma with regard to therapy for patients with these diseases (1). In the past 30 years (post-AIDS era), NTM have increasingly been associated with pulmonary diseases in humans (2). Recent studies in urban areas of the(More)
Ambient temperature plays a large role in insect growth, development and even their distribution. The elucidation of the associated molecular mechanism that underlies the effect of constant high temperature will enables us to further understand the stress responses. We constructed four digital gene expression libraries from the fat body of female and male(More)