Mutant dwarf and calorie-restricted mice benefit from healthy aging and unusually long lifespan. In contrast, mouse models for DNA repair-deficient progeroid syndromes age and die prematurely. To identify mechanisms that regulate mammalian longevity, we quantified the parallels between the genome-wide liver expression profiles of mice with those two extremes of lifespan. Contrary to expectation, we find significant, genome-wide expression associations between the progeroid and long-lived mice. Subsequent analysis of significantly over-represented biological processes revealed suppression of the endocrine and energy pathways with increased stress responses in both delayed and premature aging. To test the relevance of these processes in natural aging, we compared the transcriptomes of liver, lung, kidney, and spleen over the entire murine adult lifespan and subsequently confirmed these findings on an independent aging cohort. The majority of genes showed similar expression changes in all four organs, indicating a systemic transcriptional response with aging. This systemic response included the same biological processes that are triggered in progeroid and long-lived mice. However, on a genome-wide scale, transcriptomes of naturally aged mice showed a strong association to progeroid but not to long-lived mice. Thus, endocrine and metabolic changes are indicative of "survival" responses to genotoxic stress or starvation, whereas genome-wide associations in gene expression with natural aging are indicative of biological age, which may thus delineate pro- and anti-aging effects of treatments aimed at health-span extension.
Pubmed ID: 18704162 RIS Download
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
View all literature mentionsComputable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
View all literature mentionsInternational functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.
View all literature mentionsGD library is an open source code library for the dynamic creation of images by programmers. GD is written in C, and wrappers are available for Perl, PHP and other languages. GD creates PNG, JPEG and GIF images, among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the fly. While not restricted to use on the web, the most common applications of GD involve website development. gd is a graphics library. It allows your code to quickly draw images complete with lines, arcs, text, multiple colors, cut and paste from other images, and flood fills, and write out the result as a PNG or JPEG file. This is particularly useful in World Wide Web applications, where PNG and JPEG are two of the formats accepted for inline images by most browsers. gd is not a paint program. If you are looking for a paint program, you are looking in the wrong place. If you are not a programmer, you are looking in the wrong place, unless you are installing a required library in order to run an application. gd does not provide for every possible desirable graphics operation. It is not necessary or desirable for gd to become a kitchen-sink graphics package, but version 2.0 does include most frequently requested features, including both truecolor and palette images, resampling (smooth resizing of truecolor images) and so forth. What if I want to use another programming language? Not all of these tools are necessarily up to date and fully compatible with 2.0.33. PHP A variant of gd 2.x is included in PHP 4.3.0. It is also possible to patch PHP 4.2.3 for use with gd 2.0.33; see the gd home page for a link to that information. It would be a Good Idea to merge all of the things that are better in mainstream gd and all of the things that are better in PHP gd at some point in the near future. Perl gd can also be used from Perl, courtesy of Lincoln Stein''s GD.pm library, which uses gd as the basis for a set of Perl 5.x classes. Highly recommended. OCaml gd can be used from OCaml, thanks to Matt Gushee''s GD4O project. Tcl gd can be used from Tcl with John Ellson''s Gdtclft dynamically loaded extension package. Pascal Pascal enthusiasts should look into the freepascal project, a free Pascal compiler that includes gd support. REXX A gd interface for the REXX language is available. Any Language The fly interpreter performs gd operations specified in a text file. You can output the desired commands to a simple text file from whatever scripting language you prefer to use, then invoke the interpreter.
View all literature mentionsBioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis.
View all literature mentionsAffymetrix has recently released a new software for the acquisition, management, and analysis of gene expression data. The new GeneChip Operating Software (GCOS) platform enables researchers to perform gene expression, SNP mapping and resequencing analysis with integrated data management and scalable client server configurations. * Compatible with additional Affymetrix analysis software such as Data Mining Tool (DMT) and GeneChip DNA Analysis Software (GDAS) * Supports Gene Expression, Resequencing and Genotyping Applications * Baseline Comparison Analysis Input: Affymetrix .DAT file Output: Affymetrix files (.CEL, .CHP, .RPT, .EXP, .TXT) Availability: The Core Facility has a copy of GCOS, as well as an older version of the Affymetrix software, Microarray Suite (MAS), available for use upon request.
View all literature mentionsMus musculus with name C57BL/6J from IMSR.
View all literature mentions