MOESM3 of Intrinsic DNA curvature in trypanosomes

Additional file 3: Figure S3. Graphical representation of sequence dependent curvature in T. cruzi chromosomes. The chromosome number is depicted at the top of each page. Upper panel: Bar plots of chromosome positions with an IC value greater than 13 degrees per helical turn. Middle panel: Bar plots of chromosome positions with an RIIC value greater than the selected cutoff. Lower panel: both chromosome DNA strands are depicted in grey, overlaid with CDS features shown in blue. Features labeled as ncRNA, snRNA or snoRNAs are shown in green. tRNAs are shown in red. Assembly gaps are shown in brown

MOESM5 of Intrinsic DNA curvature in trypanosomes

Additional file 5: Figure S3. Graphical representation of transcription markers’ signals and sequence dependent curvature RIIC score in T. brucei. For each T. brucei chromosome, the graphical representation of regions with RIIC value greater than the selected cutoff (lower panel) are shown above the schematic representation of both chromosome DNA strands depicted in grey, overlaid with CDS features shown in blue. Modified histone locations (H4K10ac) from [17] and base J from [12] are indicated as following: regions associated to H4K10ac but not associated with base J (*); regions associated to H4K10ac and also with base J (!); regions associated with base J and not with H4K10ac (+). Features labeled as ncRNA, snRNA or snoRNAs are shown in green. tRNAs are shown in red. Assembly gaps are shown in brown

MOESM1 of Intrinsic DNA curvature in trypanosomes

Additional file 1: Table S1. Association between high RIIC regions and transcription markers per chromosome

Graphical representation of IC for regions with high RIIC score for three <i>L.</i><i>major</i> chromosomes.

<p>The graphs are the same as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063068#pone-0063068-g001" target="_blank">figure 1</a>. IC for regions with high RIIC score are represented on top. Asterisks mark sites defined as sites associated with acetylated H3 histone <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063068#pone.0063068-Thomas1" target="_blank">[18]</a>.</p

Comparative analysis of high RIIC regions <i>vs.</i> reported putative TSS in <i>Leishmania</i>.

<p><b>A</b>. The total number of different type of regions (D SS: Divergent Strand Switch; D T: divergent telomeres; ncRNA: associated with ncRNA transcription; I TSS: internal to polycistrons TSS) associated with TSS markers obtained in Thomas, <i>et. al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063068#pone.0063068-Thomas1" target="_blank">[18]</a> in the <i>L. major</i> genome is represented. Dark grey indicates the number of regions associated with TSS markers that overlap with high RIIC regions. <b>B</b>. Same as in A displaying in dark grey the number of regions associated with TSS markers that overlap with high RIIC regions that are present either in <i>L. major</i> or <i>L. infantum</i>.</p

Graphical representation of IC peaks on selected <i>L.</i><i>major</i> chromosomes.

<p>Bar plots of IC positions with an IC value greater than 9 degrees per helical turn. Both DNA strands are depicted in grey below bar plots, overlaid with CDS features shown in blue. Features labeled as ncRNA, snRNA or snoRNAs are shown in green. tRNAs are shown in red.</p

Regional Integrated Intrinsic Curvature analysis in <i>L.</i><i>major</i>.

<p>Bar plot showing the percentage of regions with significant RIIC score (p<0.05), indicated as highly curved, for divergent (DSSR) and convergent (CSSR) strand switch regions.</p

MOESM6 of An integrated view of the role of miR-130b/301b miRNA cluster in prostate cancer

Additional file 6: Table S1. Correlation between the expression of validated miRNA-mRNA target gene pairs in TCGA-PRAD. For each gene target the role in PrCa, reference indicated as PMID, correlation r and p value are shown. No qualifier- miR-130b directed targets with strong experimental evidence assigned by TarBase. a- miR-301b direct targets with strong experimental evidence assigned by TarBase. †-Direct Targets with experimental validation in PrCa which are not identified by TarBase. *-Direct Targets predicted in PrCa which are not identified by TarBase

MOESM3 of An integrated view of the role of miR-130b/301b miRNA cluster in prostate cancer

Additional file 3: Figure S3. Pattern of DNA methylation of the miR-130b/miR-301b locus in prostate cell lines. Methylation levels (beta-value) of the 12 CpG dinucleotide probes located along the gene obtained using the Infinium HumanMethylation450 BeadCHiP array of PrCa cell lines GSE34340, GSE62053, GSE54758 [31, 32]. The beta-value of methylation of each site is indicated. The ratio of fluorescence intensity between the unmethylated and methylated sites ranges between 0 and 1 respectively. Horizontal boxes indicate the position of the CpG island, S-shore, precursor miRNAs and POLR2A (RNA Polymerase II)

MOESM5 of An integrated view of the role of miR-130b/301b miRNA cluster in prostate cancer

Additional file 5: Figure S5. Correlation between miR-301b and target mRNAs expression in TCGA-PRAD. Scatter plots for target mRNAs highlighted in bold in Table 2, with negative (A) and positive (B) correlations. The non-parametric Spearman correlation coefficient (r) is indicated