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Reuse of public genome-wide gene expression data
Johan Rung,Alvis Brazma +1 more
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TLDR
The utility of the gene expression data that are in the public domain and how researchers are making use of these data are discussed and recommendations are provided that can improve the utility of such data.Abstract:
Our understanding of gene expression has changed dramatically over the past decade, largely catalysed by technological developments. High-throughput experiments - microarrays and next-generation sequencing - have generated large amounts of genome-wide gene expression data that are collected in public archives. Added-value databases process, analyse and annotate these data further to make them accessible to every biologist. In this Review, we discuss the utility of the gene expression data that are in the public domain and how researchers are making use of these data. Reuse of public data can be very powerful, but there are many obstacles in data preparation and analysis and in the interpretation of the results. We will discuss these challenges and provide recommendations that we believe can improve the utility of such data.read more
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Integrated View of Baseline Protein Expression in Human Tissues
TL;DR: In this paper , the authors reanalyzed 24 public proteomics datasets from healthy human individuals to assess baseline protein abundance in 31 organs and integrated the protein abundance results into the resource Expression Atlas, where they can be accessed and visualized either individually or together with gene expression data coming from transcriptomics datasets.
Journal ArticleDOI
Microarray Normalization Revisited for Reproducible Breast Cancer Biomarkers.
Michael Kenn,Dan Cacsire Castillo-Tong,Christian F. Singer,Michael Cibena,Heinz Kölbl,Wolfgang Schreiner +5 more
TL;DR: A revisit widely used data-normalization procedures and evaluates differences in outcome in order to pinpoint the most reliable reprocessing methods biomarkers can be based upon, and nominate those normalization methods yielding consistent and trustable results.
Differential drug response as a function of age
TL;DR: A systematic analysis on the ontogeny of pharmacologically relevant genes brings a new perspective on age-related differential drug responses, and challenges some of the approaches used when extrapolating knowledge from adult studies to other aged populations.
Journal ArticleDOI
Functional genomics: applications to production agriculture
Teresia Buza,Fiona M. McCarthy +1 more
TL;DR: How transcriptomics, proteomics, metabolomics, interactomics, interactionomics, epigenetics and nutrigenomics are applied to improve the understanding of complex production traits and how the environment affects these traits is looked at.
References
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M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
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TL;DR: The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data and provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-power gene expression and genomic hybridization experiments.
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