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Classification of gene signatures for their information value and functional redundancy

Laura Cantini, Laurence Calzone, Loredana Martignetti, Mattias Rydenfelt, Nils Blüthgen, Emmanuel Barillot, Andrei Zinovyev
doi: https://doi.org/10.1101/136499
Laura Cantini
1Institut Curie, INSERM U900, PSL Research University, Mines ParisTech, 26, rue d’Ulm, F-75248 Paris, France
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  • For correspondence: laura.cantini@curie.fr andrei.zinovyev@curie.fr
Laurence Calzone
1Institut Curie, INSERM U900, PSL Research University, Mines ParisTech, 26, rue d’Ulm, F-75248 Paris, France
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Loredana Martignetti
1Institut Curie, INSERM U900, PSL Research University, Mines ParisTech, 26, rue d’Ulm, F-75248 Paris, France
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Mattias Rydenfelt
2Institute of Pathology, Charite Universitätsmedizin Berlin, Chariteplatz 1, 10117 Berlin, Germany
3IRI Life Sciences and Institute for Theoretical Biology, Humboldt University, Philippstr. 13, Haus 18, 10115 Berlin, Germany
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Nils Blüthgen
2Institute of Pathology, Charite Universitätsmedizin Berlin, Chariteplatz 1, 10117 Berlin, Germany
3IRI Life Sciences and Institute for Theoretical Biology, Humboldt University, Philippstr. 13, Haus 18, 10115 Berlin, Germany
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Emmanuel Barillot
1Institut Curie, INSERM U900, PSL Research University, Mines ParisTech, 26, rue d’Ulm, F-75248 Paris, France
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Andrei Zinovyev
1Institut Curie, INSERM U900, PSL Research University, Mines ParisTech, 26, rue d’Ulm, F-75248 Paris, France
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  • For correspondence: laura.cantini@curie.fr andrei.zinovyev@curie.fr
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ABSTRACT

Large collections of gene signatures play a pivotal role in interpreting results of omics data analysis but suffer from compositional (large overlap) and functional (redundant read-outs) redundancy, and many gene signatures rarely pop-up in statistical tests. Based on pan-cancer data analysis, here we define a restricted set of 962 so called informative signatures and demonstrate that they have more chances to appear highly enriched in cancer biology studies. We show that the majority of informative signatures conserve their weights for the composing genes (eigengenes) from one cancer type to another. We construct InfoSigMap, an interactive online map showing the structure of compositional and functional redundancies between informative signatures and charting the territories of biological functions accessible through transcriptomic studies. InfoSigMap can be used to visualize in one insightful picture the results of comparative omics data analyses and suggests reconsidering existing annotations of certain reference gene set groups.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 10, 2017.
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Classification of gene signatures for their information value and functional redundancy
Laura Cantini, Laurence Calzone, Loredana Martignetti, Mattias Rydenfelt, Nils Blüthgen, Emmanuel Barillot, Andrei Zinovyev
bioRxiv 136499; doi: https://doi.org/10.1101/136499
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Classification of gene signatures for their information value and functional redundancy
Laura Cantini, Laurence Calzone, Loredana Martignetti, Mattias Rydenfelt, Nils Blüthgen, Emmanuel Barillot, Andrei Zinovyev
bioRxiv 136499; doi: https://doi.org/10.1101/136499

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