Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study

BACKGROUND: A method to evaluate and analyze the massive data generated by series of microarray experiments is of utmost importance to reveal the hidden patterns of gene expression. Because of the complexity and the high dimensionality of microarray gene expression profiles, the dimensional reduction of raw expression data and the feature selections necessary for, for example, classification of disease samples remains a challenge. To solve the problem we propose a two-level analysis. First self-organizing map (SOM) is used. SOM is a vector quantization method that simplifies and reduces the dimensionality of original measurements and visualizes individual tumor sample in a SOM component plane. Next, hierarchical clustering and K-means clustering is used to identify patterns of gene expression useful for classification of samples. RESULTS: We tested the two-level analysis on public data from diffuse large B-cell lymphomas. The analysis easily distinguished major gene expression patterns without the need for supervision: a germinal center-related, a proliferation, an inflammatory and a plasma cell differentiation-related gene expression pattern. The first three patterns matched the patterns described in the original publication using supervised clustering analysis, whereas the fourth one was novel. CONCLUSIONS: Our study shows that by using SOM as an intermediate step to analyze genome-wide gene expression data, the gene expression patterns can more easily be revealed. The "expression display" by the SOM component plane summarises the complicated data in a way that allows the clinician to evaluate the classification options rather than giving a fixed diagnosis

Correlation between vitamin A, E, coenzyme Q10 and degree of insulin resistance in obese and non-obese subjects

The aim of the present study was to investigate correlation between plasma vitamin A, vitamin E, serum coenzyme Q10 levels and degree of insulin resistance in obese and normal weight people. The study was performed on 98 (21 Male, 77 Female) obese people and 78 (20 Male, 58 Female) control subjects. Vitamin A, E and coenzyme Q10 levels were adjusted to the lipid levels. Adjusted vitamin A and E and coenzyme Q10 levels of the obese female group were significantly lower than those of the control female group. Adjusted vitamin A and coenzyme Q10 levels of the obese male group were significantly lower than those of the control male group. Insulin resistance level of the obese female and male groups were significantly higher than that of the control female and male groups. There were no significant correlations between serum coenzyme Q10, plasma vitamin A and E levels and insulin resistance in obese and control subjects. Our findings show that it is essential to use the lipid adjusted levels of lipid soluble nutrients in obesity. Also, we have found no association between insulin resistance and vitamin A, vitamin E and coenzyme Q10 levels in obese subjects

Parathyroid hormone, but not vitamin D, is associated with the metabolic syndrome in morbidly obese women and men: a cross-sectional study

<p>Abstract</p> <p>Background</p> <p>The prevalence of vitamin D insufficiency and secondary hyperparathyroidism is high among morbidly obese subjects. Further, low serum levels of 25-hydroxyvitamin D (25 [OH]D) and magnesium have been associated with increased risk of the metabolic syndrome (MS), and recently, a possible link between PTH and MS has been reported. Although it is well known that the synthesis and secretion of PTH is regulated by serum levels of calcium, phosphate, magnesium and 25(OH)D, less is known about the possible clustered affiliation of these parameters with MS. We aimed to explore whether MS is associated with abnormal serum levels of PTH, 25(OH)D and magnesium in a population of morbidly obese patients.</p> <p>Methods</p> <p>Fasting serum levels of 25(OH)D, PTH and magnesium were assessed in a cross-sectional cohort study of 1,017 consecutive morbidly obese patients (68% women). Multiple logistic regression analyses were used to assess the independent effect of PTH, 25(OH)D and magnesium on the odds for MS (National Cholesterol Education Program [NCEP]) after adjustment for confounding factors.</p> <p>Results</p> <p>Sixty-eight percent of the patients had MS. Patients with MS had lower mean serum magnesium (P < 0.001) and higher mean PTH (P = 0.067) than patients without MS, whereas mean 25(OH)D did not differ significantly. Patients with PTH levels in the second to fourth quartiles had higher odds of prevalent MS (odds ratio 1.47 [95% CI 0.92–2.35], 2.33 [95% CI 1.40–3.87] and 2.09 [95% CI 1.23–3.56], respectively), after adjustment for 25(OH)D, magnesium, calcium, phosphate, creatinine, age, gender, season of serum sampling, BMI, current smoking, albuminuria, CRP, insulin resistance and type 2 diabetes. Further, PTH was significantly correlated with systolic and diastolic pressure (both P < 0.001), but not with the other components of MS. The levels of 25(OH)D and magnesium were not associated with MS in the multivariate model.</p> <p>Conclusion</p> <p>The PTH level, but not the vitamin D level, is an independent predictor of MS in treatment seeking morbidly obese Caucasian women and men. Randomized controlled clinical trials, including different therapeutic strategies to lower PTH, e.g. calcium/vitamin D supplementation and weight reduction, are necessary to explore any cause-and-effect relationship.</p

Tinned fruit consumption and mortality in three prospective cohorts.

Dietary recommendations to promote health include fresh, frozen and tinned fruit, but few studies have examined the health benefits of tinned fruit. We therefore studied the association between tinned fruit consumption and mortality. We followed up participants from three prospective cohorts in the United Kingdom: 22,421 participants from the European Prospective Investigation into Cancer and Nutrition (EPIC)-Norfolk cohort (1993-2012), 52,625 participants from the EPIC-Oxford cohort (1993-2012), and 7440 participants from the Whitehall II cohort (1991-2012), all reporting no history of heart attack, stroke, or cancer when entering these studies. We estimated the association between frequency of tinned fruit consumption and all cause mortality (primary outcome measure) using Cox regression models within each cohort, and pooled hazard ratios across cohorts using random-effects meta-analysis. Tinned fruit consumption was assessed with validated food frequency questionnaires including specific questions about tinned fruit. During 1,305,330 person years of follow-up, 8857 deaths occurred. After adjustment for lifestyle factors and risk markers the pooled hazard ratios (95% confidence interval) of all cause mortality compared with the reference group of tinned fruit consumption less often than one serving per month were: 1.05 (0.99, 1.12) for one to three servings per month, 1.10 (1.03, 1.18) for one serving per week, and 1.13 (1.04, 1.23) for two or more servings per week. Analysis of cause-specific mortality showed that tinned fruit consumption was associated with mortality from cardiovascular causes and from non-cardiovascular, non-cancer causes. In a pooled analysis of three prospective cohorts from the United Kingdom self-reported tinned fruit consumption in the 1990s was weakly but positively associated with mortality during long-term follow-up. These findings raise questions about the evidence underlying dietary recommendations to promote tinned fruit consumption as part of a healthy diet.EPIC-Norfolk is supported by the Medical Research Council (grant numbers G1000143, G0401527, G9502233, G0300128) and Cancer Research UK (grant numbers C864/A14136, C865/A2883). EPIC-Oxford is supported by Cancer Research UK (C570/A11691). Whitehall II has been supported by grants from the Medical Research Council; the British Heart Foundation; the British Health and Safety Executive; the British Department of Health; the National Heart, Lung, and Blood Institute (R01HL036310); and the National Institute on Aging at the US National Institutes of Health (NIH). ETA is supported by an academic clinical fellowship awarded by the United Kingdom National Institute for Health Research. EB is funded by the British Heart Foundation. MAHL received grants from Cancer Research UK, and Medical Research Council. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.This is the final published version. It first appeared in PLoS ONE 10(2): e0117796. doi: 10.1371/journal.pone.0117796

Mutational dynamics and immune evasion in diffuse large B-cell lymphoma explored in a relapse-enriched patient series

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