Significance analysis of microarray transcript levels in time series experiments

Background: Microarray time series studies are essential to understand the dynamics of molecular events. In order to limit the analysis to those genes that change expression over time, a first necessary step is to select differentially expressed transcripts. A variety of methods have been proposed to this purpose; however, these methods are seldom applicable in practice since they require a large number of replicates, often available only for a limited number of samples. In this data-poor context, we evaluate the performance of three selection methods, using synthetic data, over a range of experimental conditions. Application to real data is also discussed. Results: Three methods are considered, to assess differentially expressed genes in data-poor conditions. Method 1 uses a threshold on individual samples based on a model of the experimental error. Method 2 calculates the area of the region bounded by the time series expression profiles, and considers the gene differentially expressed if the area exceeds a threshold based on a model of the experimental error. These two methods are compared to Method 3, recently proposed in the literature, which exploits splines fit to compare time series profiles. Application of the three methods to synthetic data indicates that Method 2 outperforms the other two both in Precision and Recall when short time series are analyzed, while Method 3 outperforms the other two for long time series. Conclusion: These results help to address the choice of the algorithm to be used in data-poor time series expression study, depending on the length of the time series

Association of education with dietary intake among young adults in the bi-ethnic Coronary Artery Risk Development in Young Adults (CARDIA) cohort

OBJECTIVE: To examine associations of changes in dietary intake with education in young black and white men and women. DESIGN: The Coronary Artery Risk Development in Young Adults (CARDIA) study, a multi-centre population-based prospective study. Dietary intake data at baseline and year 7 were obtained from an extensive nutritionist-administered diet history questionnaire with 700 items developed for CARDIA. SETTING: Participants were recruited in 1985-1986 from four sites: Birmingham, Alabama; Chicago, Illinois; Minneapolis, Minnesota; and Oakland, California. SUBJECTS: Participants were from a general community sample of 703 black men (BM), 1006 black women (BW), 963 white men (WM) and 1054 white women (WW) who were aged 18-30 years at baseline. Analyses here include data for baseline (1985-1986) and year 7 (1992-1993). RESULTS: Most changes in dietary intake were observed among those with high education (\u3eor=12 years) at both examinations. There was a significant decrease in intake of energy from saturated fat and cholesterol and a significant increase in energy from starch for each race-gender group (P\u3c0.001). Regardless of education, taste was considered an important influence on food choice. CONCLUSION: The inverse relationship of education with changes in saturated fat and cholesterol intakes suggests that national public health campaigns may have a greater impact among those with more education

Positive psychosocial factors may protect against perceived stress in people with systemic lupus erythematosus with and without trauma history

Objective: Trauma history is associated with SLE onset and worse patient-reported outcomes; perceived stress is associated with greater SLE disease activity. Stress perceptions vary in response to life events and may be influenced by psychosocial factors. In an SLE cohort, we examined whether stressful events associated with perceived stress, whether psychosocial factors affected perceived stress, and whether these relationships varied by prior trauma exposure. Methods: This is a cross-sectional analysis of data from the California Lupus Epidemiology Study, an adult SLE cohort. Multivariable linear regression analyses controlling for age, gender, educational attainment, income, SLE damage, comorbid conditions, glucocorticoids ≥7.5 mg/day and depression examined associations of recent stressful events (Life Events Inventory) and positive (resilience, self-efficacy, emotional support) and negative (social isolation) psychosocial factors with perceived stress. Analyses were stratified by lifetime trauma history (Brief Trauma Questionnaire (BTQ)) and by adverse childhood experiences (ACEs) in a subset. Results: Among 242 individuals with SLE, a greater number of recent stressful events was associated with greater perceived stress (beta (95% CI)=0.20 (0.07 to 0.33), p=0.003). Positive psychosocial factor score representing resilience, self-efficacy and emotional support was associated with lower perceived stress when accounting for number of stressful events (−0.67 (−0.94 to –0.40), p<0.0001); social isolation was associated with higher stress (0.20 (0.14 to 0.25), p<0.0001). In analyses stratified by BTQ trauma and ACEs, associations of psychosocial factors and perceived stress were similar between groups. However, the number of recent stressful events was significantly associated with perceived stress only for people with BTQ trauma (0.17 (0.05 to 0.29), p=0.0077) and ACEs (0.37 (0.15 to 0.58), p=0.0011).Conclusion: Enhancing positive and lessening negative psychosocial factors may mitigate deleterious perceived stress, which may improve outcomes in SLE, even among individuals with a history of prior trauma who may be more vulnerable to recent stressful events

Significance analysis of microarray transcript levels in time series experiments-2

<p><b>Copyright information:</b></p><p>Taken from "Significance analysis of microarray transcript levels in time series experiments"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S10</p><p>BMC Bioinformatics 2007;8(Suppl 1):S10-S10.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885839.</p><p></p>se positives divided by the number of selected genes for different number of selected genes (right panels) obtained on 100 simulated data sets, using methods 1, 2 and 3 on time series of 10 (upper left panel), 30 (upper right panel), and 50 (lower left panel) samples. AUCs are also reported for Precision vs Recall curves

Significance analysis of microarray transcript levels in time series experiments-0

<p><b>Copyright information:</b></p><p>Taken from "Significance analysis of microarray transcript levels in time series experiments"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S10</p><p>BMC Bioinformatics 2007;8(Suppl 1):S10-S10.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885839.</p><p></p>ene expression studies. Samples are collected from an insulin treated and a control culture. The expression level measured in treated and control culture for a single probe-set (corresponding to "Early growth response 1" gene) is shown in the lower part of the Figure. The area A bounded by the two expression profiles T and C is coloured in gray

Race, Ethnicity, and Disparities in the Risk of End‐Organ Lupus Manifestations Following a Systemic Lupus Erythematosus Diagnosis in a Multiethnic Cohort

ObjectiveData on the onset of lupus manifestations across multiple organ domains and in diverse populations are limited. The objective was to analyze racial and ethnic differences in the risk of end-organ lupus manifestations following systemic lupus erythematosus (SLE) diagnosis in a multiethnic cohort.MethodsThe California Lupus Epidemiology Study (CLUES) is a longitudinal study of SLE. Data on major end-organ lupus manifestations were collected and categorized by organ system: renal, hematologic, neurologic, cardiovascular, and pulmonary. Multiorgan disease was defined as manifestations in ≥2 of these distinct organ systems. Kaplan-Meier curves assessed end-organ disease-free survival, and Cox proportional hazards regression estimated the rate of end-organ disease following SLE diagnosis, adjusting for age at diagnosis, sex, and self-reported race and ethnicity (White, Hispanic, Black, and Asian).ResultsOf 326 participants, 89% were female; the mean age was 45 years. Self-reported race and ethnicity were 30% White, 23% Hispanic, 11% Black, and 36% Asian. Multiorgan disease occurred in 29%. Compared to White participants, Hispanic and Asian participants had higher rates, respectively, of renal (hazard ratio [HR] 2.9 [95% confidence interval (95% CI) 1.8-4.7], HR 2.9 [95% CI 1.9-4.6]); hematologic (HR 2.7 [95% CI 1.3-5.7], HR 2.1 [95% CI 1.0-4.2]); and multiorgan disease (HR 3.3 [95% CI 1.8-5.9], HR 2.5 [95% CI 1.4-4.4]) following SLE diagnosis.ConclusionWe found heightened risks of developing renal, hematologic, and multiorgan disease following SLE diagnosis among Hispanic and Asian patients with SLE, as well as a high burden of multiorgan disease among CLUES participants

Causes of Death Among Individuals With Systemic Lupus Erythematosus by Race and Ethnicity: A Population‐Based Study

ObjectiveNon-White populations are at higher risk of developing systemic lupus erythematosus (SLE) and have more severe outcomes, including mortality. The present study was undertaken to examine how specific causes of death vary by race and ethnicity, including Asian and Hispanic individuals.MethodsThe California Lupus Surveillance Project included SLE cases identified among residents of San Francisco County, CA during January 1, 2007 to December 31, 2009. Cases were matched to the National Death Index over a 10-year period. Logistic regression examined age-adjusted differences in causes of death by race, ethnicity, and sex. Age-standardized mortality ratios between individuals with SLE and the corresponding general population were calculated for the leading cause of death, and observed versus expected deaths were estimated.ResultsThe study included 812 individuals of White (38%), Asian (36%), Black (20%), and mixed/other/unknown (5%) race; 15% identified as Hispanic. One hundred thirty-five deaths were recorded, with a mean ± SD age at death of 62.2 ± 15.6 years. Cardiovascular disease (CVD) was the leading cause of death overall (33%), and across all racial and ethnic groups, followed by rheumatic disease (18%) and hematologic/oncologic conditions (18%). CVD as the underlying cause of death was 3.63 times higher among SLE cases than in the general population. CVD deaths for those with SLE were nearly 4 and 6 times higher for Asian and Hispanic individuals with SLE, respectively, compared to the general population.ConclusionIndividuals with SLE experience a disproportionate burden of CVD mortality compared to the general population, which is magnified for Asian and Hispanic groups