ArticleGenomics, proteomics & bioinformatics2006
High-sensitivity transcriptome data structure and implications for analysis and biologic interpretation.
Article in Genomics, proteomics & bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
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- Latent HIV-1 TAR Regulates 7SK-responsive P-TEFb Target Genes and Targets Cellular Immune Responses in the Absence of Tat.Genomics, proteomics & bioinformatics · 2017Article
- HIC1 controls cellular- and HIV-1- gene transcription via interactions with CTIP2 and HMGA1.Scientific reports · 2016Article
- Airway structural cells regulate TLR5-mediated mucosal adjuvant activity.Mucosal immunology · 2014Article
- HMGA1 recruits CTIP2-repressed P-TEFb to the HIV-1 and cellular target promoters.Nucleic acids research · 2014Article
- A TDG/CBP/RARα ternary complex mediates the retinoic acid-dependent expression of DNA methylation-sensitive genes.Genomics, proteomics & bioinformatics · 2014Article
- Alternative splicing of TAF6: downstream transcriptome impacts and upstream RNA splice control elements.PloS one · 2014Article
- CTIP2 is a negative regulator of P-TEFb.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- CDS: a fold-change based statistical test for concomitant identification of distinctness and similarity in gene expression analysis.Genomics, proteomics & bioinformatics · 2012Article
- A network perspective on metabolic inconsistency.BMC systems biology · 2012Article
- 7SK small nuclear RNA directly affects HMGA1 function in transcription regulation.Nucleic acids research · 2011Article
- Quality assessment of transcriptome data using intrinsic statistical properties.Genomics, proteomics & bioinformatics · 2010Article
- Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response.The Journal of clinical investigation · 2009Article
- EBER2 RNA-induced transcriptome changes identify cellular processes likely targeted during Epstein Barr Virus infection.BMC research notes · 2008Article
- Determining the impact of alternative splicing events on transcriptome dynamics.BMC research notes · 2008Article
- Article
- Generation of synthetic transcriptome data with defined statistical properties for the development and testing of new analysis methods.Genomics, proteomics & bioinformatics · 2007Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Novel microarray technologies such as the AB1700 platform from Applied Biosystems promise significant increases in the signal dynamic range and a higher sensitivity for weakly expressed transcripts. We have compared a representative set of AB1700 data with a similarly representative Affymetrix HG-U133A dataset. The AB1700 design extends the signal dynamic detection range at the lower bound by one order of magnitude. The lognormal signal distribution profiles of these high-sensitivity data need to be represented by two independent distributions. The additional second distribution covers those transcripts that would have gone undetected using the Affymetrix technology. The signal-dependent variance distribution in the AB1700 data is a non-trivial function of signal intensity, describable using a composite function. The drastically different structure of these high-sensitivity transcriptome profiles requires adaptation or even redevelopment of the standard microarray analysis methods. Based on the statistical properties, we have derived a signal variance distribution model for AB1700 data that is necessary for such development. Interestingly, the dual lognormal distribution observed in the AB1700 data reflects two fundamentally different biologic mechanisms of transcription initiation.
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