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date Sun, 03 Dec 2023 12:51:54 +0000
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1 <p><head>
2 <title>RBPBench - Search Report</title></p>
3 <script src="/home/uhlm/Programme/miniconda3/envs/rbpbench/lib/python3.11/site-packages/rbpbench/content/sorttable.js" type="text/javascript"></script>
4 <p></head></p>
5 <h1>Search report</h1>
6 <p>List of available statistics and plots generated
7 by RBPBench (rbpbench search --report):</p>
8 <ul>
9 <li><a href="#rbp-enrich-stats">RBP motif enrichment statistics</a></li>
10 <li><a href="#cooc-heat-map">RBP co-occurrences heat map</a></li>
11 <li><a href="#corr-heat-map">RBP correlations heat map</a>
12 &nbsp;</li>
13 </ul>
14 <h2 id="rbp-enrich-stats">RBP motif enrichment statistics</h2>
15 <p><strong>Table:</strong> RBP motif enrichment statistics. Given a score for each genomic region (# input regions = 1),
16 RBPbench checks whether motifs are enriched
17 in higher-scoring regions (using Wilcoxon rank-sum test). A low Wilcoxon rank-sum test p-value for a given RBP thus indicates
18 that higher-scoring regions are more likely to contain motif hits of the respective RBP. NOTE that if scores associated to
19 input genomic regions are all the same, p-values become meaningless (i.e., they result in p-values of 1.0).</p>
20 <table class="sortable">
21 <thead>
22 <tr>
23 <th style="text-align: center;">RBP ID</th>
24 <th style="text-align: center;"># hit regions</th>
25 <th style="text-align: center;">% hit regions</th>
26 <th style="text-align: center;"># motif hits</th>
27 <th style="text-align: center;">p-value</th>
28 </tr>
29 </thead>
30 <tbody>
31 <tr>
32 <td style="text-align: center;">PUM1</td>
33 <td style="text-align: center;">1</td>
34 <td style="text-align: center;">100.00</td>
35 <td style="text-align: center;">1</td>
36 <td style="text-align: center;">1.0</td>
37 </tr>
38 <tr>
39 <td style="text-align: center;">PUM2</td>
40 <td style="text-align: center;">1</td>
41 <td style="text-align: center;">100.00</td>
42 <td style="text-align: center;">4</td>
43 <td style="text-align: center;">1.0</td>
44 </tr>
45 </tbody>
46 </table>
47 <p>&nbsp;
48 &nbsp;</p>
49 <p>Column IDs have the following meanings: <strong>RBP ID</strong> -&gt; RBP ID from database or user-defined (typically RBP name), <strong># hit regions</strong> -&gt; number of input genomic regions with motif hits (after filtering and optional extension), <strong>% hit regions</strong> -&gt; percentage of hit regions over all regions (i.e. how many input regions contain &gt;= 1 RBP binding motif), <strong># motif hits</strong> -&gt; number of unique motif hits in input regions (removed double counts), <strong>p-value</strong> -&gt; Wilcoxon rank-sum test p-value.</p>
50 <h2 id="cooc-heat-map">RBP co-occurrences heat map</h2>
51 <p>RBP co-occurrences heat map.</p>
52 <div class=class="container-fluid" style="margin-top:40px">
53 <iframe src="html_report_plots/co-occurrence_plot.plotly.html" width="1200" height="1200"></iframe>
54 </div>
55
56 <p><strong>Figure:</strong> Heat map of co-occurrences (Fisher's exact test p-values) between RBPs.
57 Legend color: negative logarithm (base 10) of Fisher's exact test p-value.
58 Hover box: 1) RBP1. 2) RBP2. 3) p-value: Fisher's exact test p-value (calculated based on contingency table between RBP1 and RBP2).
59 4) RBPs compaired. 5) Counts[]: Contingency table of co-occurrence counts (i.e., number of genomic regions with/without shared motif hits) between compaired RBPs,
60 with format [[A, B], [C, D]], where
61 A: RBP1 AND RBP2,
62 B: NOT RBP1 AND RBP2
63 C: RBP1 AND NOT RBP2
64 D: NOT RBP1 AND NOT RBP2. </p>
65 <p>&nbsp;</p>
66 <h2 id="corr-heat-map">RBP correlations heat map</h2>
67 <p>RBP correlations heat map.</p>
68 <div class=class="container-fluid" style="margin-top:40px">
69 <iframe src="html_report_plots/correlation_plot.plotly.html" width="1200" height="1200"></iframe>
70 </div>
71
72 <p><strong>Figure:</strong> Heat map of correlations (Pearson correlation coefficients) between RBPs.
73 Genomic regions are labelled 1 or 0 (RBP motif present or not), resulting in a vector of 1s and 0s for each RBP.
74 Correlations are then calculated by comparing vectors for every pair of RBPs.
75 Legend color: Pearson correlation coefficient.
76 Hover box: 1) RBP1. 2) RBP2.
77 3) RBPs compaired. 5) Counts[]: Contingency table of co-occurrence counts (i.e., number of genomic regions with/without shared motif hits) between compaired RBPs,
78 with format [[A, B], [C, D]], where
79 A: RBP1 AND RBP2,
80 B: NOT RBP1 AND RBP2
81 C: RBP1 AND NOT RBP2
82 D: NOT RBP1 AND NOT RBP2. </p>
83 <p>&nbsp;</p>