| Title: | PaintOmics 4 : new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases |
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| Authors: | ID Liu, Tianyuan (Author)
ID Salguero, Pedro (Author)
ID Petek, Marko (Author)
ID Martinez-Mira, Carlos (Author)
ID Balzano-Nogueira, Leandro (Author)
ID Ramšak, Živa (Author)
ID McIntyre, Lauren (Author)
ID Gruden, Kristina (Author)
ID Tarazona, Sonia (Author)
ID Conesa, Ana (Author) |
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| Files: |  URL - Source URL, visit https://doi.org/10.1093/nar/gkac352
 PDF - Presentation file, download (3,53 MB)
MD5: 3B6A31A08FF7A627A2447A7E593E8DE1
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| Language: | English |
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| Typology: | 1.01 - Original Scientific Article |
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| Organization: |  NIB - National Institute of Biology
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| Abstract: | PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology. |
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| Keywords: | PaintOmics 4, web tools, datasets, analysis methods, molecular biology |
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| Publication version: | Version of Record |
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| Publication date: | 24.05.2022 |
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| Year of publishing: | 2022 |
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| Number of pages: | str. W551-W559 |
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| Numbering: | Vol. 50, iss. W1 |
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| PID: | 20.500.12556/DiRROS-19337  |
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| UDC: | 577 |
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| ISSN on article: | 0305-1048 |
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| DOI: | 10.1093/nar/gkac352 |
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| COBISS.SI-ID: | 110574851 |
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| Note: | Ostali avtorji: Pedro Salguero, Marko Petek, Carlos Martinez-Mira, Leandro Balzano-Nogueira, Živa Ramšak, Lauren McIntyre, Kristina Gruden, Sonia Tarazona, Ana Conesa;
Članek v PDF formatu obsega 9 str.;
First online: 24 May 2022;
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| Publication date in DiRROS: | 17.07.2024 |
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| Views: | 303 |
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| Downloads: | 223 |
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