Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.

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Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.

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limma powers differential expression analyses for RNA-sequencing and microarray studies

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

http://www.klinikaikozpont.u-szeged.hu/pedia/images/pdf/CME_TEL/Full-Text/25.pdf

The Hallmarks of Aging

Obesity alters adipose tissue metabolic and endocrine function and leads to an increased release of fatty acids, hormones, and proinflammatory molecules that contribute to obesity associated complications. To further characterize the changes that occur in adipose tissue with increasing adiposity, we profiled transcript expression in perigonadal adipose tissue from groups of mice in which adiposity varied due to sex, diet, and the obesity-related mutations agouti (Ay) and obese (Lepob). We found that the expression of 1,304 transcripts correlated significantly with body mass. Of the 100 most significantly correlated genes, 30% encoded proteins that are characteristic of macrophages and are positively correlated with body mass. Immunohistochemical analysis of perigonadal, perirenal, mesenteric, and subcutaneous adipose tissue revealed that the percentage of cells expressing the macrophage marker F4/80 (F4/80+) was significantly and positively correlated with both adipocyte size and body mass. Similar relationships were found in human subcutaneous adipose tissue stained for the macrophage antigen CD68. Bone marrow transplant studies and quantitation of macrophage number in adipose tissue from macrophage-deficient (Csf1op/op) mice suggest that these F4/80+ cells are CSF-1 dependent, bone marrow-derived adipose tissue macrophages. Expression analysis of macrophage and nonmacrophage cell populations isolated from adipose tissue demonstrates that adipose tissue macrophages are responsible for almost all adipose tissue TNF-alpha expression and significant amounts of iNOS and IL-6 expression. Adipose tissue macrophage numbers increase in obesity and participate in inflammatory pathways that are activated in adipose tissues of obese individuals.

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Obesity is associated with macrophage accumulation in adipose tissue

Nature 532, 112–116 (2016); doi:10.1038/nature17399 In this Letter, owing to a typographical error, Fig. 4h was erroneously referred to as Fig. 4j in the text and in the Fig. 4 legend. This error has been corrected online.

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Corrigendum: Mitochondrial ROS regulate thermogenic energy expenditure and sulfenylation of UCP1.

In accordance with the present invention, it has been discovered that PPARη is expressed consistently in each of the major histologic types of human liposarcoma. It has further been discovered that maximal activation of PPARη with exogenous ligand (a thiazolidinedione or derivative thereof) promotes terminal differentiation of primary human liposarcoma cells. It has still further been discovered that RXR-specific ligands are also potent adipogenic agents in cells expressing the PPARη/RXRα heterodimer, and that simultaneous treatment of liposarcoma cells with a thiazolidinedionyl moiety (a PPARη-selective class of compounds) and an RXR-specific ligand results in an additive stimulation of differentiation. Accordingly, according to the invention, there have been identified compositions which are useful for the treatment of liposarcomas.

Treatment of liposarcomas using a combination of thiazolidinediones and retinoid x receptor selective agonists

Methods are disclosed to stimulate angiogenesis in a warm-blooded animal, which method comprises administering to a subject in need of such treatment, an amount of an angiogenic glyceride of formulae (1) or (2) wherein X is O, NH, S, or CH2, and R1 is alkyl (1-10C) or acyl (2-10C) which is saturated or unsaturated and which is unsubstituted or substituted with one or more substituents which do not interfere with angiogenic activity, said substituents selected from the group consisting of OH, OR, SH, SR, NH?2?, NHR, NR2 and halo wherein each R is independently lower alkyl (1-4C); and each of R?2 and R3? is independently H, PO?3?-2, or is alkyl or acyl as defined above, or in formula 1, R?2 and R3? taken together are an alkylene moiety or OR?2 and OR3? form an epoxide. The compounds of formulae (1) or (2) or mixtures thereof can be used in combination with various peptide growth factors to enhance the angiogenesis effect.

Angiogenic monobutyrin and its analogs

The invention provides compositions and methods for regulating thermogenesis and muscle inflammation through modulation of Metrnl and/or Metrn activity and/or expression. Also provided are methods for preventing or treating metabolic disorders and muscle inflammation disorders in a subject through modulation of Metrnl and/or Metrn activity and/or expression. Further provided are methods for identifying compounds that are capable of treating metabolic disorders and muscle inflammation disorders by modulating Metrnl and/or Metrn activity and/or expression.

Bruce M. Spiegelman

Papers

Corrigendum: Mitochondrial ROS regulate thermogenic energy expenditure and sulfenylation of UCP1.

Treatment of liposarcomas using a combination of thiazolidinediones and retinoid x receptor selective agonists

Angiogenic monobutyrin and its analogs

Compositions and methods for regulating thermogenesis and muscle inflammation using metrnl and metrn

Role and Regulation of PPARy During Adipogenesis