Gene Set Enrichment Analysis (GSEA) is a computational method that assesses whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. We report the availability of a new version of the Java based software (GSEA-P 2.0) that represents a major improvement on the previous release through the addition of a leading edge analysis component, seamless integration with the Molecular Signature Database (MSigDB) and an embedded browser that allows users to search for gene sets and map them to a variety of microarray platform formats. This functionality makes it possible for users to directly import gene sets from MSigDB for analysis with GSEA. We have also improved the visualizations in GSEA-P 2.0 and added links to a new form of concise gene set annotations called Gene Set Cards. These additions, as well as other improvements suggested by over 3500 users who have downloaded the software over the past year have been incorporated into this new release of the GSEA-P Java desktop program. Availability: GSEA-P 2.0 is freely available for academic and commercial users and can be downloaded from http://www.broad.
The abundance of genomic data now available in biomedical research has stimulated the development of sophisticated statistical methods for interpreting the data, and of special visualization tools for displaying the results in a concise and meaningful manner. However, biologists often find these methods and tools difficult to understand and use correctly. GenePattern is a freely available software package that addresses this issue by providing more than 100 analysis and visualization tools for genomic research in a comprehensive user‐friendly environment for users at all levels of computational experience and sophistication. This unit demonstrates how to prepare and analyze microarray data in GenePattern. Curr. Protoc. Bioinform. 22:7.12.1–7.12.39. © 2008 by John Wiley & Sons, Inc.
In February 2007, U.S. media outlets covered the coming out of retired NBA player John Amaechi, one of only 6 professional male athletes from the four major U.S. team sports to have announced that he is gay. This study analyzes newspaper columns by prominent U.S. sportswriters about Amaechi's announcement. Textual analysis found that although the columns could be read as progressive, they were not; they condemned individuals who expressed overtly homophobic views while reinforcing the status quo in a variety of ways. The neo-homophobic discourse can be compared with that of new racism, a strategy that maintain racial hegemony in the U.S. As such, these columns effectively rendered Amaechi's announcement as having little value in addressing homophobia in the sports/media complex.
Beer drinking has long been valorised as a masculine performance and a social ritual. But as more women enter the craft beer industry, new opportunities emerge to reframe the cultural discourses around beer. With an interest in the stories women brewers ('brewsters') tell, we conducted interviews (n ¼ 6), and a textual analysis of brand strategies (n ¼ 10) used by women-owned beer brands in New Zealand. With an attention towards how gender identity factors into these narratives, we found that women largely reproduce the narrative trope of 'authenticity' utilised by craft brewers broadly. Gender identity is largely rendered invisible at the expense of promoting authenticity as a seemingly gender-neutral value. In New Zealand, however, these strategies must be contextualised in a cultural history in which beer drinking and national identity are fundamentally intertwined, and in ways that have has always been coded masculine. Our findings suggest that while branding can potentially enhance the visibility of women as legitimate producers of beer, New Zealand brewsters maintain craft beer as a P akeh a (White European) middle-class masculine cultural form.
This project explores consumer evaluations on Yelp.com as ''commodity activism'' -the politicization of market activities for the purposes of social change and/or cultural resistance. A textual analysis of consumer evaluations (n ¼ 1972) and interviews (n ¼ 18) reveal that commodity activism on Yelp most commonly appears as a positive bias toward localism. Consumers discursively construct an aesthetic of authenticity around localism that functions in accordance with the logic of corporate branding; in turn, ''brand local'' is appropriated by reviewers as part of their own authentic ''self-brand'' grounded in the civic duty to one's community. The implications of this logic are critiqued against commodity activism's commitment to individual, personalized forms of self-empowerment over identification with larger collective and community struggles. In this sense, Yelp is favorable to neoliberal discourses of consumer capitalism, where consumption serves as a stand-in for citizenship and localism's political potential reconfigured in market terms.
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