Additional file 1 of UniBind: maps of high-confidence direct TF-DNA interactions across nine species
Creators: name: Puig, Rafael Riudavets
name: Boddie, Paul
name: Khan, Aziz
name: Castro-Mondragon, Jaime Abraham
name: Mathelier, Anthony
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Overview of the permissive collection. Table providing the number of datasets, TFs, cell / tissue types, and TFBSs in the permissive collection of UniBind. The number of TFBSs was computed as the number of unique instances of genomic loci bound by a TF. Table S2. Overview of the robust collection. Table providing the number of datasets, TFs, cell /tissue types, and TFBSs in the robust collection of UniBind. The number of TFBSs was computed as the number of unique instances of genomic loci bound by a TF. Figure S1. Visual overview of the permissive collection. (A) Barplots showing the number of TFs (dark orange), TFBSs (green), datasets (blue), and cell and tissue types (light orange) stored in the permissive collection of UniBind for each analyzed species. All values are log10-transformed. (B) Distribution of the percentages of the genomes covered by robust TFBSs in each species (one color per species, see legend). Figure S2. Relationship between number of datasets and genome coverage. Scatter plots representing the percentage of genome coverage (y-axes) with respect to the number of datasets in the permissive (A) and robust (C) collections or the number of TFs in the permissive (B) and robust (D) collection (x-axes). Each colored point in each panel represents the data associated to one species (see legend for color coding). Figure S3. The UniBind 2021 compressed and robust tracks with all TFBSs from the robust human collection. An example of a random genomic locus showing the comparison between the original and archetypal TFBSs. The tracks shown are, from top to bottom: RefSeq track with the first intron of the human TTC6 gene, the UniBind compressed track with archetypal TFBSs, and the UniBind robust track showing all TFBSs at the same location. Figure S4. Evolutionary conservation at human and mouse robust CRMs. Distributions of the average base-pair evolutionary conservation scores (phyloP and phastCons scores using multi-species genome alignments, see legend) at regions centered around UniBind human (A) and mouse (B) CRMs from the robust collection. Conservation of random CRMs was obtained by shuffling the original CRMs and obtaining the conservation score of the new regions. Figure S5. Enrichment analysis for A. thaliana TFBSs in genomic regions. Barplots representing the expected (grey bars) versus observed (blue bars) overlap lengths (A) or number of intersections (B) between A. thaliana TFBSs from the robust collection and genomic annotations (x-axis). The plots and computed p-values (green: enrichment; orange: depletion) were obtained using the OLOGRAM command of the GTF toolkit. Figure S6. Enrichment analysis for C. elegans TFBSs in genomic regions. Barplots representing the expected (grey bars) versus observed (blue bars) overlap lengths (A) or number of intersections (B) between C. elegans TFBSs from the robust collection and genomic annotations (x-axis). The plots and computed p-values (green: enrichment; orange: depletion) were obtained using the OLOGRAM command of the GTF toolkit. Figure S7. Enrichment analysis for D. rerio TFBSs in genomic regions. Barplots representing the expected (grey bars) versus observed (blue bars) overlap lengths (A) or number of intersections (B) between D. rerio TFBSs from the robust collection and genomic annotations (x-axis). The plots and computed p-values (green: enrichment; orange: depletion) were obtained using the OLOGRAM command of the GTF toolkit. Figure S8. Enrichment analysis for D. melanogaster TFBSs in genomic regions. Barplots representing the expected (grey bars) versus observed (blue bars) overlap lengths (A) or number of intersections (B) between D. melanogaster TFBSs from the robust collection and genomic annotations (x-axis). The plots and computed p-values (green: enrichment; orange: depletion) were obtained using the OLOGRAM command of the GTF toolkit. Figure S9. Enrichment analysis for R. norvegicus TFBSs in genomic regions. Barplots representing the expected (grey bars) versus observed (blue bars) overlap lengths (A) or number of intersections (B) between R. norvegicus TFBSs from the robust collection and genomic annotations (x-axis). The plots and computed p-values (green: enrichment; orange: depletion) were obtained using the OLOGRAM command of the GTF toolkit. Figure S10. Enrichment analysis for S. cerevisae TFBSs in genomic regions. Barplots representing the expected (grey bars) versus observed (blue bars) overlap lengths (A) or number of intersections (B) between S. cerevisae TFBSs from the robust collection and genomic annotations (x-axis). The plots and computed p-values (green: enrichment; orange: depletion) were obtained using the OLOGRAM command of the GTF toolkit. Figure S11. Analysis of the overlap of robust TFBSs with respect to genomic annotations in all species in UniBind. Fraction of TFBSs in the UniBind robust collection (y-axis) with respect to increasing relative distances (x-axis) from different genomic regions computed using the bedtools reldist command. When two genomic tracks are not spatially related, one expects the fraction of relative distance distribution to be uniform. Figure S12. Genomic distribution of TFBSs in A. thaliana, C. elegans and D. rerio. Distribution of the proportion of A. thaliana, C. elegans and D. rerio UniBind robust TFBSs overlapping with different types of genomic regions (colors; see legend) across TFs (columns). Figure S13. Genomic distribution of TFBSs in D. melanogaster and H. sapiens. Distribution of the proportion of D. melanogaster and H. sapiens UniBind robust TFBSs overlapping with different types of genomic regions (colors; see legend) across TFs (columns). Figure S14. Genomic distribution of TFBSs in H. sapiens (continued) and M. musculus. Distribution of the proportion of H. sapiens (continued) and M. musculus UniBind robust TFBSs overlapping with different types of genomic regions (colors; see legend) across TFs (columns). Figure S15. Genomic distribution of TFBSs in M. musculus (continued). Distribution of the proportion of M. musculus (continued) UniBind robust TFBSs overlapping with different types of genomic regions (colors; see legend) across TFs (columns). Figure S16. Genomic distribution of TFBSs in R. norvegicus and S. cerevisiae. Distribution of the proportion of R. norvegicus and S. cerevisiae UniBind robust TFBSs overlapping with different types of genomic regions (colors; see legend) across TFs (columns). Figure S17. Enrichment analysis for H. sapiens TFBSs in ENCODE cCREs. Barplots representing the expected (grey bars) versus observed (blue bars) overlap lengths (A) or number of intersections (B) between H. sapiens TFBSs from the robust collection and ENCODE cCREs (x-axis). The plots and computed p-values (green: enrichment; orange: depletion) were obtained using the OLOGRAM command of the GTF toolkit. Figure S18. Enrichment analysis for M. musculus TFBSs in ENCODE cCREs. Barplots representing the expected (grey bars) versus observed (blue bars) overlap lengths (A) or number of intersections (B) between M. musculus TFBSs from the robust collection and ENCODE cCREs (x-axis). The plots and computed p-values (green: enrichment; orange: depletion) were obtained using the OLOGRAM command of the GTF toolkit. Figure S19. Enrichment analysis for H. sapiens CRMs in ENCODE cCREs. Barplots representing the expected (grey bars) versus observed (blue bars) overlap lengths (A) or number of intersections (B) between H. sapiens CRMs from the robust collection and ENCODE cCREs (x-axis). The plots and computed p-values (green: enrichment; orange: depletion) were obtained using the OLOGRAM command of the GTF toolkit. Figure S20. Enrichment analysis for M. musculus CRMs in ENCODE cCREs. Barplots representing the expected (grey bars) versus observed (blue bars) overlap lengths (A) or number of intersections (B) between M. musculus CRMs from the robust collection and ENCODE cCREs (x-axis). The plots and computed p-values (green: enrichment; orange: depletion) were obtained using the OLOGRAM command of the GTF toolkit. Figure S21. Relative distance distributions between CRMs and ENCODE cCREs. Fraction of CRMs in the UniBind robust collection (y-axis) with respect to increasing relative distances (x-axis) from ENCODE cCREs computed using the bedtools reldist command for human (A) and mouse (B). When two genomic tracks are not spatially related, one expects the fraction of relative distance distribution to be uniform. Figure S22. Correlation between enhancer activity and TF binding. For each enhancer predicted using Cap Analysis of Gene Expression (CAGE) by the FANTOM5 consortium, we computed the number of TFs with overlapping TFBSs in the robust collection of UniBind (x-axis). The figure provides, for each value of the number of TFs found to bind in enhancers, the median (blue line) together with the 10th to 90th percentiles (grey area) of tissue specific activity of these enhancers. The expression measures were derived from CAGE (capturing enhancer RNA expression). The specificity of activity (y-axis) is provided within the [0; 1] range with 0 representing ubiquitous enhancer activity and 1 exclusive expression activity.