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| 1 | Normalization Using Weighted Negative Second Order Exponential Error Functions(NeONORM) Provides Robustness Against Asym-metries in Comparative Transcriptome Profiles and Avoids False Calls显示文摘Studies on high-throughput global gene expression using microarray technology have generated ever larger amounts of systematic transcriptome data. A major challenge in exploiting these heterogeneous datasets is how to normalize the expres- sion profiles by inter-assay methods. Different non-linear and linear normalization methods have been developed, which essentially rely on the hypothesis that the true or perceived logarithmic fold-change distributions between two different assays are symmetric in nature. However, asymmetric gene expression changes are fre- quently observed, leading to suboptimal normalization results and in consequence potentially to thousands of false calls. Therefore, we have specifically investigated asymmetric comparative transcriptome profiles and developed the normalization using weighted negative second order exponential error functions (NeONORM) for robust and global inter-assay normalization. NeONORM efficiently damps true gene regulatory events in order to minimize their misleading impact on the nor- malization process. We evaluated NeONORM’s applicability using artificial and true experimental datasets, both of which demonstrated that NeONORM could be systematically applied to inter-assay and inter-condition comparisons. | Sebastian Noth Guillaume Brysbaert Arndt Benecke | 2006 | Genomics, Proteomics & Bioinformatics2006，4，2： | 4 |
| 2 | High-Sensitivity Transcriptome Data Structure and Implications for Analysis and Biologic Interpretation显示文摘Novel microarray technologies such as the AB1700 platform from Applied Biosys-tems promise significant increases in the signal dynamic range and a higher sensi-tivity for weakly expressed transcripts. We have compared a representative set ofAB1700 data with a similarly representative Affymetrix HG-U133A dataset. TheAB1700 design extends the signal dynamic detection range at the lower bound byone order of magnitude. The lognormal signal distribution profiles of these high-sensitivity data need to be represented by two independent distributions. Theadditional second distribution covers those transcripts that would have gone unde-tected using the Affymetrix technology. The signal-dependent variance distribu-tion in the AB1700 data is a non-trivial function of signal intensity, describableusing a composite function. The drastically different structure of these high-sensitivity transcriptome profiles requires adaptation or even redevelopment ofthe standard microarray analysis methods. Based on the statistical properties, wehave derived a signal variance distribution model for AB1700 data that is neces-sary for such development. Interestingly, the dual lognormal distribution observedin the AB1700 data reflects two fundamentally different biologic mechanisms oftranscription initiation. | Sebastian Noth Guillaume Brysbaert Franois-Xavier Pellay Arndt Benecke | 2006 | Genomics, Proteomics & Bioinformatics2006，4，4： | 3 |
| 3 | Quality Assessment of Transcriptome Data Using Intrinsic Statistical Properties显示文摘In view of potential application to biomedical diagnosis,tight transcriptome data quality control is compulsory.Usually,quality control is achieved using labeling and hybridization controls added at different stages throughout the processing of the biologic RNA samples.These control measures,however,only reflect the performance of the individual technical manipulations during the entire process and have no bearing as to the continued integrity of the RNA sample itself.Here we demonstrate that intrinsic statistical properties of the resulting transcriptome data signal and signal-variance distributions and their invariance can be identified independently of the animal species studied and the labeling protocol used.From these invariant properties we have developed a data model,the parameters of which can be estimated from individual experiments and used to compute relative quality measures based on similarity with large reference datasets.These quality measures add supplementary,non-redundant information to standard quality control estimates based on spike-in and hybridization controls,and are exploitable in data analysis.A software application for analyzing datasets as well as a reference dataset for AB1700 arrays are provided.They should allow AB1700 users to easily integrate this method into their analysis pipeline,and might instigate similar developments for other transcriptome platforms. | Guillaume Brysbaert Franois-Xavier Pellay Sebastian Noth Arndt Benecke | 2010 | Genomics, Proteomics & Bioinformatics2010，8，1： | 2 |
| 4 | 2+ 2- : a new high-nitrogen high-energetic material 显示文摘 | Hammerl A Klapotke T M Noth H | 2001 | Inorg Chem2001，40，： | 1 |
| 5 | Prophylaxis of heterotopic ossification after total hip arthroplasty: a prospective randomized study comparing indomethacin and meloxicam 显示文摘 | Barthel T Baumann B Noth U | 2002 | Acta Orthop Scand2002，73，6： | 1 |
| 6 | IL-4 upregulates IL-1-induced chemokine gene expression in bone marrow stromal cells by enhancing NF-κB activation显示文摘 | Pindolia KR Noth CJ Xu YX | 1996 | Hematopathol Mol Hematol1996，10，4： | 1 |
| 7 | Cartilage Development, Physiology,Pathologies,and Regeneration显示文摘 | Wang X Rackwitz L Noth U | | 0，，： | 1 |
| 8 | Design of an ultralight weight autonomous solar airplane for continuous flight显示文摘 | NOTH A ENGEL W SIEGWART R | 2006 | Proceedings of Field and Service Robotics2006，25，7： | 1 |
| 9 | Repeated use of the GnRH analogue deslorelin to down-regulate reproduction in male cheetahs (Acinanyx jubatus) 显示文摘 | Bertschinger HT Jago I Nothing Jo | 2006 | Thrigenology2006，66，： | 1 |
| 10 | Functional switch between motor tracts in the presence of the mAb IN-1 in the adult rat显示文摘 | Raineteau O Fouad K Noth P | 2001 | Proc Natl Acad Sci USA2001，98，12： | 1 |
| 11 | CT findings and clinical features as markers for patient outcome in primary pontine hemorrhage 显示文摘 | Wessels T Moller-Hartmann W Noth J | 2004 | AJNR2004，25，2： | 1 |
| 12 | CT findings and clinical features as markers for patient outcome in wary pontinc hemorrhage 显示文摘 | Wcsscls T Mollcr-HatmannW Noth J | 2004 | Am J Neuroradiol2004，，： | 1 |
| 13 | A placbo-controlled randomized trial of warfarin in idiopathic pulmonary fibrosis显示文摘 | Noth I Anstrom KJ Calvert SB | 2012 | Am J Respir Crit Care Med2012，186，1： | 1 |
| 14 | Pervaporation separation of water-ethanol through modified chitosan membranes(Ⅱ)显示文摘 | Lee Y M Shin E M Noth S T | 1991 | Die Angewandte Makromolekulare Chemie1991，192，1： | 1 |
| 15 | Peripheral blood biomarkers in idiopathic pulmonary fibrosis显示文摘 | Vij R Noth I | 2012 | Transl Res2012，159，4： | 1 |
| 16 | A placebo--controlledran- domized trial of warfarin in idiopathic pulmonaryfibrosis显示文摘 | Noth 1 Anstrom K J Calvert SB | 2012 | Am J Respir Crit Care Med2012，186，1： | 1 |
| 17 | Effects of NiO addition in WO3-based gas sensors prepared by thick film process显示文摘 | NOTH W SHIN Y KIM J | 2002 | Solid State Ionics2002，，14： | 1 |
| 18 | Incorporation of cholesterolinto the cellular membrane of Lactobacillus acidohilus ATCC43121 显示文摘 | NOTH D KIM S H GILLILAND S E | 1997 | J Dairy Sci1997，82，： | 1 |
| 19 | A placebo-controlled randomized trial of warfarin in idiopathic pulmonary fibrosis显示文摘 | Noth I Anstrom KJ Calvert SB | 2012 | Am J Respir Crit Care Med2012，186，1： | 1 |
| 20 | In vitro engineered cartilage constructs produced by press-coating biodegradable polymer with human mesenchymal stem cells显示文摘 | NOTH U TULI R OSYCZKA A M | 2002 | Tissue Eng2002，8，1： | 1 |
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