研究課題

An Excel file containing information on lncRNAs probed for FM bias. The first sheet contains a README file with details on the contents of the other two sheets. The second sheet contains the list of all lncRNAs probed, a summary of their biological function, and the original source from which we extracted them. The third sheet contains the FM bias p value computed for each significantly FM biased lncRNA in each cohort. (ODS 13 kb

Alu elements vs splice sites in the graphics.plot() output (A) and in the visualize() output (B).

<p>Alu elements are consistently located at a variable but always nonzero distance from splice sites. Query and reference colors as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002529#pcbi-1002529-g001" target="_blank">Figure 1</a>.</p

Continued summary of correlations performed in the experiments described.

*<p>∼0 means that the default R precision for the binomial test is not enough to distinguish the value from 0.</p><p>P-values are shown for all tests in both directions (using one dataset as the query and the other as the reference, then reversing). For each test, we have indicated whether the relationship between the datasets is positive or negative; for the relative and absolute distance tests this is written as “close (C)” vs “far (F)” and for the Jaccard and projection tests it is written as “overlapping (O)” vs “nonoverlapping (N).”</p

NFkappaB sites vs human RefSeq promoter start sites.

<p>Query and reference colors as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002529#pcbi-1002529-g001" target="_blank">Figure 1</a>. (A) NFkappaB as the query gives a significant Kolmogorov-Smirnov association and anticorrelation that is visible from the graph, in absolute distances. (B) Correlation in the reverse direction suggests no significant relationship between the two classes of sites.</p

A schematic of the various tests implemented in the software package, showing when certain tests are most useful.

<p>(A) depicts the intervals created in silico and (B) shows how the query distances are evaluated within the intervals. (C) depicts a random distribution of query versus reference intervals; here the observed and expected distances for both the absolute and relative tests are the same. In (D) we show a relationship best uncovered by the absolute distance test; useful especially for small genomes, this test determines whether the query and reference are often separated by a fixed distance. In (E), the query points are consistently far away from the reference points, so the relative distance test will be significant, while the absolute distances are not significant in this case. Interestingly, the query intervals are variable enough in size that even though the query and reference points are usually separated, the absolute distances between them vary widely in size, including some fairly small distances. (F) demonstrates the projection test, which evaluates whether pointwise data falls consistently inside or outside of a set of intervals. Finally, in (G) we see the Jaccard test, which looks for significant overlaps between datasets by evaluating the ratio of the intersection of the datasets (dark grey) to the union of the datasets (light grey). Perfect correlation will give a ratio of 1, and perfect anticorrelation will result in a ratio of zero.</p

A toy example of absolute distance correlation.

<p>(A) Histograms of the observed and expected ranges of minimum distances between the reference and query. (B) GenometriCorr's simple plot for the same data. Query and reference colors as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002529#pcbi-1002529-g001" target="_blank">Figure 1</a>.</p

Summary of all correlations performed in these experiments.

*<p>∼0 means that the default R precision for KS test p-value is not enough to distinguish the value from 0.</p

Ty1 retrotransposon insertion sites vs tRNA genes in the yeast genome.

<p>(A) ECDF plots (B) Graphic display. Arrows mark Ty1 insertion sites at nucleosome-occupied positions near tRNA genes. Nucleosomes are in green. The colored graph contains several regions of high observed/expected Ty1 insertions (red colors), and the black line indicates a high density of Ty1 insertions, as well, in these regions. Relative to the tRNA position, the Ty1 insertion sites are most dense inside the nucleosome occupied regions. Query and reference colors as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002529#pcbi-1002529-g001" target="_blank">Figure 1</a>.</p

Two types of graphic output are available.

<p>(A) A statistical summary and ECDF plots. (B) A graphical interpretation of the spatial relationships. The query features are depicted along the plot according to their distance to a reference feature; the colors indicate deviation from the expected distribution while the overlay line indicates the density of the data at each absolute or relative distance. The data density mirrors but is independent from the log-odds colors; at small distances in the absolute distance plot the data density is higher than expected but this represents a very small percentage of the total query points.</p

Promoter positions from highly expressed genes (as given from mRNAseq data) and histone ChIP data recently available from the Roadmap Epigenomics Project [<b>8</b>].

<p>(A) H3K4me3 versus highly expressed genes. (B) H3K27me3 versus highly expressed genes. Query and reference colors as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002529#pcbi-1002529-g001" target="_blank">Figure 1</a>.</p