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  Effect of imputation on gene network reconstruction from single-cell RNA-seq data

Ly, L.-H., & Vingron, M. (2022). Effect of imputation on gene network reconstruction from single-cell RNA-seq data. Patterns, 3: 100414. doi:10.1016/j.patter.2021.100414.

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Patterns_Ly and Vingron_2021.pdf (Verlagsversion), 3MB
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© 2021 The Author(s)

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 Urheber:
Ly, Lam-Ha1, Autor           
Vingron, Martin1, Autor           
Affiliations:
1Transcriptional Regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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Schlagwörter: imputation gene regulation network reconstruction network inference single-cell data analysis single-cell RNA-seq
 Zusammenfassung: Despite the advances in single-cell transcriptomics, the reconstruction of gene regulatory networks remains challenging. Both the large amount of zero counts in experimental data and the lack of a consensus preprocessing pipeline for single-cell RNA sequencing (scRNA-seq) data make it hard to infer networks. Imputation can be applied in order to enhance gene-gene correlations and facilitate downstream analysis. However, it is unclear what consequences imputation methods have on the reconstruction of gene regulatory networks. To study this, we evaluate the differences on the performance and structure of reconstructed networks before and after imputation in single-cell data. We observe an inflation of gene-gene correlations that affects the predicted network structures and may decrease the performance of network reconstruction in general. However, within the modest limits of achievable results, we also make a recommendation as to an advisable combination of algorithms while warning against the indiscriminate use of imputation before network reconstruction in general.

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Sprache(n): eng - English
 Datum: 2021-11-252022-02-11
 Publikationsstatus: Online veröffentlicht
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 Ort, Verlag, Ausgabe: -
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 Identifikatoren: DOI: 10.1016/j.patter.2021.100414
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Titel: Patterns
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: Amsterdam : Elsevier
Seiten: - Band / Heft: 3 Artikelnummer: 100414 Start- / Endseite: - Identifikator: ISSN: 2666-3899
CoNE: https://pure.mpg.de/cone/journals/resource/2666-3899