Altenbuchinger, M. and Schwarzfischer, P. and Rehberg, T. and Reinders, J. and Kohler, Ch. W. and Gronwald, W. and Richter, J. and Szczepanowski, M. and Masque-Soler, N. and Klapper, W. and Oefner, P. J. and Spang, R. (2017) Molecular signatures that can be transferred across different omics platforms. BIOINFORMATICS, 33 (14). I333-I340. ISSN 1367-4803, 1460-2059
Full text not available from this repository. (Request a copy)Abstract
Motivation: Molecular signatures for treatment recommendations are well researched. Still it is challenging to apply them to data generated by different protocols or technical platforms. Results: We analyzed paired data for the same tumors (Burkitt lymphoma, diffuse large B-cell lymphoma) and features that had been generated by different experimental protocols and analytical platforms including the nanoString nCounter and Affymetrix Gene Chip transcriptomics as well as the SWATH and SRM proteomics platforms. A statistical model that assumes independent sample and feature effects accounted for 69-94% of technical variability. We analyzed how variability is propagated through linear signatures possibly affecting predictions and treatment recommendations. Linear signatures with feature weights adding to zero were substantially more robust than unbalanced signatures. They yielded consistent predictions across data from different platforms, both for transcriptomics and proteomics data. Similarly stable were their predictions across data from fresh frozen and matching formalin-fixed paraffin-embedded human tumor tissue.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | B-CELL LYMPHOMA; PARAFFIN-EMBEDDED TISSUE; GENE-EXPRESSION; VARIABLE SELECTION; MASS-SPECTROMETRY; BURKITTS-LYMPHOMA; CLASSIFICATION; REGULARIZATION; REGRESSION; PROTEOMICS; |
| Subjects: | 600 Technology > 610 Medical sciences Medicine |
| Divisions: | Medicine > Institut für Funktionelle Genomik > Lehrstuhl für Funktionelle Genomik (Prof. Oefner) Medicine > Institut für Funktionelle Genomik > Lehrstuhl für Statistische Bioinformatik (Prof. Spang) |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 14 Dec 2018 13:16 |
| Last Modified: | 20 Feb 2019 15:09 |
| URI: | https://pred.uni-regensburg.de/id/eprint/1539 |
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