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Israel T Silva Ricardo ZN Vêncio Thiago YK Oliveira Greice A Molfetta Wilson A SilvaJr 《BMC bioinformatics》2010,11(1):161
Background
The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regulation under distinct biological conditions and can be performed by analyzing the Multiple Differential Expression (MDE) of genes associated with normal and abnormal biological processes. Currently MDE analyses are limited to usual methods of differential expression initially designed for paired analysis. 相似文献2.
Background
The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. 相似文献3.
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Background
As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. 相似文献6.
Flávia R Rocha Flávia S Papini-Terzi Milton Y Nishiyama Jr Ricardo ZN Vêncio Renato Vicentini Rodrigo DC Duarte Vicente E de Rosa Jr Fabiano Vinagre Carla Barsalobres Ane H Medeiros Fabiana A Rodrigues Eugênio C Ulian Sônia M Zingaretti João A Galbiatti Raul S Almeida Antonio VO Figueira Adriana S Hemerly Marcio C Silva-Filho Marcelo Menossi Gláucia M Souza 《BMC genomics》2007,8(1):1-22
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