Figure 1. PaintOmics 3 workflow diagram

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Figure 1. PaintOmics 3 workflow diagram Figure 1. PaintOmics 3 workflow diagram. PaintOmics 3 takes as input tab delimited files containing processed data from ... Figure 1. PaintOmics 3 workflow diagram. PaintOmics 3 takes as input tab delimited files containing processed data from different omic types. After mapping to KEGG database and resolving metabolite ambiguities, a global analysis interface allows filtering, network and enrichment analysis of pathways. Selected pathways can be further analyzed in pathway maps displaying omic data trends and feature-level heatmaps of multi-omic measurements. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue W1, 25 May 2018, Pages W503–W509, https://doi.org/10.1093/nar/gky466 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 2. The interactive pathway network in PaintOmics 3 Figure 2. The interactive pathway network in PaintOmics 3. The interactive network panel (A) is complemented by a ... Figure 2. The interactive pathway network in PaintOmics 3. The interactive network panel (A) is complemented by a secondary panel showing the trends for all pathway clusters in a given omic (B), or the trends for each omic in the chosen pathway (C). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue W1, 25 May 2018, Pages W503–W509, https://doi.org/10.1093/nar/gky466 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 3. Workspace for pathway exploration in PaintOmics 3 Figure 3. Workspace for pathway exploration in PaintOmics 3. The layout for pathway exploration is divided into three ... Figure 3. Workspace for pathway exploration in PaintOmics 3. The layout for pathway exploration is divided into three panels. The main panel (A) contains the interactive pathway diagram, the Global Heatmap panel (B) displays multi-omics data in the form of heatmaps, and the Pathway Information panel (C) contains search and summarizing functions. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue W1, 25 May 2018, Pages W503–W509, https://doi.org/10.1093/nar/gky466 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 4. Part of the results for the PaintOmics pathway enrichment analysis for Cacchiarelli’s data (complete list in ... Figure 4. Part of the results for the PaintOmics pathway enrichment analysis for Cacchiarelli’s data (complete list in Supplementary Figure S5). The enriched pathways are ordered by the combined P-value. Upper positions correspond to the most significant pathways. A color scale is used to highlight the level of enrichment for each pathway where the higher the intensity of red, the higher the significance. Gray cells indicate that the corresponding omic data type is not present in the pathway. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue W1, 25 May 2018, Pages W503–W509, https://doi.org/10.1093/nar/gky466 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 5. Pathway networks and cluster profiles of representative temporal patterns. Network A is colored according to ... Figure 5. Pathway networks and cluster profiles of representative temporal patterns. Network A is colored according to gene expression data. Network B is colored according to H3K4me3 ChIP-seq data. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue W1, 25 May 2018, Pages W503–W509, https://doi.org/10.1093/nar/gky466 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 6. Interactive KEGG diagram for Signaling pathways regulating pluripotency of stem cells. Data obtained from ... Figure 6. Interactive KEGG diagram for Signaling pathways regulating pluripotency of stem cells. Data obtained from Cacchiarelli’s multi-omics study Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue W1, 25 May 2018, Pages W503–W509, https://doi.org/10.1093/nar/gky466 The content of this slide may be subject to copyright: please see the slide notes for details.