Figure 1. The scheme of RCAS

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Figure 1. The scheme of RCAS Figure 1. The scheme of RCAS. RCAS is composed of several components: annotation summary, coverage profile, GO term analysis, gene set enrichment and motif discovery. The individual components employ various R functions. The modular design provides options for switching on/off the individual components. The output of RCAS is a dynamic HTML consisting of interactive figures and tables, which are downloadable and ready for the purpose of publication. From: RCAS: an RNA centric annotation system for transcriptome-wide regions of interest Nucleic Acids Res. 2017;45(10):e91. doi:10.1093/nar/gkx120 Nucleic Acids Res | © The Author(s) 2017. 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 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

Figure 2. A screenshot of the Galaxy interface for RCAS Figure 2. A screenshot of the Galaxy interface for RCAS. Options are provided for inputs and switches for running individual components. From: RCAS: an RNA centric annotation system for transcriptome-wide regions of interest Nucleic Acids Res. 2017;45(10):e91. doi:10.1093/nar/gkx120 Nucleic Acids Res | © The Author(s) 2017. 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 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

Figure 3. A screenshot of the interface of the RCAS web service. From: RCAS: an RNA centric annotation system for transcriptome-wide regions of interest Nucleic Acids Res. 2017;45(10):e91. doi:10.1093/nar/gkx120 Nucleic Acids Res | © The Author(s) 2017. 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 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

Figure 4. The coverage profiles of PUM2 (A), QKI (B), IGF2BP1–3 (C) at TSS/TES. The three types of RBPs all appear to have the stronger binding preference at TES. Each coverage profile is represented with a ribbon where a solid line passing through the middle area. The solid lines represent the mean coverage score distribution and the thickness of the ribbons represents the 95% confidence interval (equal to 1.96 times the standard error of the mean). From: RCAS: an RNA centric annotation system for transcriptome-wide regions of interest Nucleic Acids Res. 2017;45(10):e91. doi:10.1093/nar/gkx120 Nucleic Acids Res | © The Author(s) 2017. 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 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

Figure 5. The coverage profiles of m<sup>1</sup>A across different features (A), at TSS/TES (B), at exon-intron boundaries (C). (A) At the promoters, the peak of coverage is at the 3΄ end of the regions. At 5΄ UTRs, the peak is at the 5΄ end of the regions. (B) m<sup>1</sup>A is clearly enriched at TSS. (C) m<sup>1</sup>A show a stark contrast between adjacent exonic and intronic regions. Each coverage profile is represented with a ribbon with a solid line passing through the middle of the ribbon. The solid lines in the middle of each coverage profile represent the mean coverage score distribution and the thickness of the ribbons encapsulating the solid line represents the 95% confidence interval (equal to 1.96 times the standard error of the mean). From: RCAS: an RNA centric annotation system for transcriptome-wide regions of interest Nucleic Acids Res. 2017;45(10):e91. doi:10.1093/nar/gkx120 Nucleic Acids Res | © The Author(s) 2017. 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 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

Figure 6. The coverage profiles of tiRNAs across different genomic features (A), at TSS/TES (B). (A) tiRNs are enriched at the 3΄ end of promoters while peak at 5΄ end of the regions of 5΄ UTRs. (B) tiRNAs are clearly enriched at TSS. Each coverage profile is represented with a ribbon where a solid line passing through the middle area. The solid lines represent the mean coverage score distribution and the thickness of the ribbons represents the 95% confidence interval (equal to 1.96 times the standard error of the mean). From: RCAS: an RNA centric annotation system for transcriptome-wide regions of interest Nucleic Acids Res. 2017;45(10):e91. doi:10.1093/nar/gkx120 Nucleic Acids Res | © The Author(s) 2017. 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 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

Figure 7. (A) The distribution of HOT regions across gene features Figure 7. (A) The distribution of HOT regions across gene features. (B) Binned coverage profiles of HOT regions overlaid on gene features. (C) Nucleotide resolution coverage profiles of HOT regions overlaid on TSS/TES boundaries. (D) Nucleotide resolution coverage profiles of HOT regions overlaid on 5΄ and 3΄ boundaries of internal exons. Each coverage profile is represented with a ribbon where a solid line passing through the middle area. The solid lines represent the mean coverage score distribution and the thickness of the ribbons represents the 95% confidence interval (equal to 1.96 times the standard error of the mean). From: RCAS: an RNA centric annotation system for transcriptome-wide regions of interest Nucleic Acids Res. 2017;45(10):e91. doi:10.1093/nar/gkx120 Nucleic Acids Res | © The Author(s) 2017. 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 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