False discovery rate, sensitivity and sample size for microarray studies

Pawitan, Yudi; Michiels, Stefan; Koscielny, Serge; Gusnanto, Arief; Ploner, Alexander

doi:10.1093/bioinformatics/bti448

Cited by 403 publications

(299 citation statements)

References 32 publications

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“…Expression levels were analysed in a multi-class response using significance analysis of microarray (Tusher et al, 2001). In total, 372 differentially expressed genes between the three analysed genotypes were statistically significant, with a false discovery rate of 4.18% meaning that among these 372 genes, 15 should be false positive (Pawitan et al, 2005). Respectively, 100% and more than 77% of the genes classed as differentially expressed, differed in expression by more than 1.5 Â and 2 Â .…”

Section: Resultsmentioning

confidence: 99%

Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm

et al. 2009

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Polyploid plants often produce new phenotypes, exceeding the range of variability existing in the diploid gene pool. Several hundred citrus allotetraploid hybrids have been created by somatic hybridization. These genotypes are interesting models to study the immediate effects of allopolyploidization on the regulation of gene expression. Here, we report genome-wide gene expression analysis in fruit pulp of a Citrus interspecific somatic allotetraploid between C. reticulata cv 'Willowleaf mandarin' þ C. limon cv 'Eureka lemon', using a Citrus 20K cDNA microarray. Around 4% transcriptome divergence was observed between the two parental species, and 212 and 160 genes were more highly expressed in C. reticulata and C. limon, respectively. Differential expression of certain genes was confirmed by quantitative real-time RT-PCR. A global downregulation of the allotetraploid hybrid transcriptome was observed, as compared with a theoretical mid parent, for the genes displaying interspecific expression divergence between C. reticulata and C. limon. The genes underexpressed in mandarin, as compared with lemon, were also systematically repressed in the allotetraploid. When genes were overexpressed in C. reticulata compared with C. limon, the distribution of allotetraploid gene expression was far more balanced. Cluster analysis on the basis of gene expression clearly indicated the hybrid was much closer to C. reticulata than to C. limon. These results suggest there is a global dominance of the mandarin transcriptome, in consistence with our previous studies on aromatic compounds and proteomics. Interspecific differentiation of gene expression and non-additive gene regulation involved various biological pathways and different cellular components.

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Section: Resultsmentioning

confidence: 99%

Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm

et al. 2009

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“…It is notable that all the cytoarchitectural traits were more significantly decreased in the bipolar disorder group as compared with the other two groups and as compared with the unaffected controls; thus, it is not surprising that more genes would show a significant correlation with trait in the bipolar and control samples. Nevertheless, genomewide microarray studies with relatively small sample sizes are prone to yielding results with low statistical power; 38 therefore, a larger sample size will be required to obtain replicable results for disorderspecific correlations.…”

Section: Discussionmentioning

confidence: 99%

Correlation analysis between genome-wide expression profiles and cytoarchitectural abnormalities in the prefrontal cortex of psychiatric disorders

2008

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Cytoarchitectural abnormalities have been described in the prefrontal cortex of subjects with schizophrenia, bipolar disorder and depression. However, little is known about the gene expression profiles associated with these abnormalities. Genome-wide expression profiling technology provides an unbiased approach to identifying candidate genes and biological processes that may be associated with complex biological traits such as cytoarchitecture. In this study, we explored expression profiles associated with the abnormalities by using publicly available microarray metadata and cytoarchitectural data from post-mortem samples of the frontal cortex from 54 subjects (schizophrenia, n = 14; bipolar disorder, n = 13; depression, n = 12 and controls n = 15). Correlation analysis between genome-wide expression levels and cytoarchitectural traits revealed that 818 genes were significantly correlated with a decrease in the number of perineuronal oligodendrocytes across all subjects. A total of 600 genes were significantly correlated with a decrease in density of calbindin-positive interneurons across all subjects. Multiple biological processes including cellular metabolism, central nervous system development, cell motility and programmed cell death were significantly overrepresented in both correlated gene lists. These findings may provide novel insights into the molecular mechanisms that underlie the cytoarchitectural abnormalities of perineuronal oligodendrocytes and calbindin-containing GABAergic interneurons in the prefrontal cortex of the major psychiatric disorders.

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“…Statistical differences between continuous variables versus the bivariate outcome variables (wound status and HO formation) were evaluated using the Mann-Whitney U test and the post hoc TukeyKramer assessment. The levels of significance for the demographic and wound-specific data were adjusted using the Bonferroni method and for the proteomic data using the false discovery rate method [14]. Associations between categorical variables were compared using Fisher's exact test or chi-square analysis, depending on the number of expected values in the contingency matrix.…”

Section: Clinical and Radiographic Followupmentioning

confidence: 99%

Do Inflammatory Markers Portend Heterotopic Ossification and Wound Failure in Combat Wounds?

Forsberg

Potter

Polfer

et al. 2014

Clinical Orthopaedics &Amp; Related Research

107

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Background After a decade of war in Iraq and Afghanistan, we have observed an increase in combat-related injury survival and a paradoxical increase in injury severity, mainly because of the effects of blasts. These severe injuries have a devastating effect on each patient's immune system resulting in massive upregulation of the systemic inflammatory response. By examining inflammatory mediators, preliminary data suggest that it may be possible to correlate complications such as wound failure and heterotopic ossification (HO) with distinct systemic and local inflammatory profiles, but this is a relatively new topic. Questions/purposes We asked whether systemic or local markers of inflammation could be used as an objective means, independent of demographic and subjective factors, to estimate the likelihood of (1) HO and/or (2) wound failure (defined as wounds requiring surgical débridement after definitive closure, or wounds that were not closed or covered within 21 days of injury) in patients sustaining combat wounds. Methods Two hundred combat wounded active-duty service members who sustained high-energy extremity The institution of one or more of the authors (JAF) has received, during the study period, funding from a grant from the Orthopaedic Trauma Research Program (OTRP) and the US Navy Bureau of Medicine and Surgery Advance Medical Development Program. All ICMJE Conflict of Interest Forms for authors and Clinical Orthopaedics and Related Research editors and board members are on file with the publication and can be viewed on request. Clinical Orthopaedics and Related Research neither advocates nor endorses the use of any treatment, drug, or device. Readers are encouraged to always seek additional information, including FDAapproval status, of any drug or device prior to clinical use. Each author certifies that his or her institution approved the human protocol for this investigation, that all investigations were conducted in conformity with ethical principles of research, and that informed consent for participation in the study was obtained. This work was performed at the Naval Medical Research Center, Silver Spring, MD, USA, and the National Military Medical Center, Bethesda, MD, USA. The views expressed this article are those of the authors and do not necessarily reflect the official policy or position of the Department of the Navy, Department of Defense, nor the U.S. Government. This study protocol was approved by the Institutional Review Boards at both the National Military Medical Center and Naval Medical Research Center in compliance with all applicable Federal regulations governing the protection of human subjects. One or more of the authors is a military service member (or employee of the U.S. Government). This work was prepared as part of his or her official duties. Title 17 U.S.C §105 provides that 'Copyright protection under this title is not available for any work of the United States Government.' Title 17 U.S.C §101 defines a U.S. Government work as a work prepared by a military service ...

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False discovery rate, sensitivity and sample size for microarray studies

Cited by 403 publications

References 32 publications

Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm

Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm

Correlation analysis between genome-wide expression profiles and cytoarchitectural abnormalities in the prefrontal cortex of psychiatric disorders

Do Inflammatory Markers Portend Heterotopic Ossification and Wound Failure in Combat Wounds?

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