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Auflistung nach Autor:in "Futschik, Matthias E."

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  • Konferenzbeitrag
    Are we overestimating the number of cell-cycling genes? The impact of background models for time series data
    (German conference on bioinformatics – GCB 2007, 2007) Futschik, Matthias E.; Herzel, Hanspeter
    Periodic processes play fundamental roles in organisms. Prominent examples are the cell cycle and the circadian clock. Microarray array technology has enabled us to screen complete sets of transcripts for possible association with such fundamental periodic processes on a system-wide level. Frequently, quite a large number of genes has been detected as periodically expressed. However, the small overlap of identified genes between different studies has shaded considerable doubts about the reliability of the detected periodic expression. In this study, we show that a major reason for the lacking agreement is the use of an inadequate background model for the determination of significance. We demonstrate that the choice of background model has considerable impact on the statistical significance of periodic expression. For illustration, we reanalyzed two microarray studies of the yeast cell cycle. Our evaluation strongly indicates that the results of previous analyses might have been overoptimistic and that the use of more suitable background model promises to give more realistic results.
  • Konferenzbeitrag
    Comparison of human protein-protein interaction maps
    (German Conference on Bioinformatics, 2006) Futschik, Matthias E.; Chaurasia, Gautam; Wanker, Erich; Herzel, Hanspeter
    Large-scale mappings of protein-protein interactions have started to give us new views of the complex molecular mechanisms inside a cell. After initial projects to systematically map protein interactions in model organisms such as yeast, worm and fly, researchers have begun to focus on the mapping of the human interactome. To tackle this enormous challenge, different approaches have been proposed and pursued. While several large-scale human protein interaction maps have recently been published, their quality remains to be critically assessed. We present here a first comparative analysis of eight currently available large-scale maps with a total of over 10000 unique proteins and 57000 interactions included. They are based either on literature search, orthology or by yeast-two-hybrid assays. Comparison reveals only a small, but statistically significant overlap. More importantly, our analysis gives clear indications that all interaction maps suffer under selection and detection biases. These results have to be taken into account for future assembly of the human interactome.