9de039a7dceb056ccfa604e0ac38e0bb901ef1ec max Mon Mar 30 17:11:20 2026 -0700 MPRA track updates, #34284 diff --git src/hg/makeDb/trackDb/human/hg38/mprabase.html src/hg/makeDb/trackDb/human/hg38/mprabase.html new file mode 100644 index 00000000000..837554a8c0c --- /dev/null +++ src/hg/makeDb/trackDb/human/hg38/mprabase.html @@ -0,0 +1,129 @@ +<h2>Description</h2> +<p> +Massively Parallel Reporter Assays (MPRAs) and related methods such as STARR-seq +enable quantitative testing of thousands of candidate regulatory DNA sequences in +parallel by linking each sequence to a reporter gene and measuring transcriptional +output using sequencing. +</p> + +<p> +The <b>MPRA Base</b> track shows 41,275 experimentally tested cis-regulatory elements +from the <a href="http://mprabase.ucsf.edu/app/mprabase" target="_blank">MPRA Base</a> +database +(<a href="https://pubmed.ncbi.nlm.nih.gov/38045264/" target="_blank">Zhao et al., 2023</a>). +The database integrates data from multiple studies, assay platforms (lentiMPRA, +plasmidMPRA, STARR-seq, CRE-seq, and others), and cell types while preserving +experiment-level resolution. Only elements derived from genomic fragments that can +be mapped to the reference genome are included; synthetic or designed oligonucleotide +libraries without genomic coordinates are excluded. +</p> + +<h2>Display Conventions</h2> +<p> +Each item represents a genomic fragment tested within a specific experiment, defined +as a unique combination of cell line, assay type, and publication (PMID). The same +genomic region may appear multiple times if tested in different experiments. +</p> + +<p> +Items are colored by percentile rank of the mean raw activity score within each experiment: +</p> +<ul> +<li><span style="color:blue;"><b>Blue</b></span> — percentile < 50</li> +<li><span style="color:orange;"><b>Orange</b></span> — percentile 50–74</li> +<li><span style="color:red;"><b>Red</b></span> — percentile ≥ 75</li> +</ul> + +<p> +The mouse-over shows the cell line, assay type, raw activity score, percentile rank, +and citation for each element. +</p> + +<h2>Methods</h2> +<p> +Within each experiment, replicate measurements for the same genomic fragment were +aggregated by computing the mean raw activity score. The original dataset contained +211,053 replicate-level measurements; after aggregation, the final track contains +41,275 unique experiment-level genomic elements. +</p> + +<p> +Elements are ranked by mean raw activity score independently within each experiment, +and a percentile rank (0–100) is computed per experiment to avoid cross-study +distortions caused by differing assay dynamic ranges. +</p> + +<h2>Experiments</h2> +<p> +The following table lists the experiments represented in this track. +</p> + +<table class="stdTbl"> +<tr> + <th>PMID</th> + <th>Author</th> + <th>Year</th> + <th>Lab</th> + <th>Cell type</th> + <th>Assay</th> + <th>Elements</th> +</tr> +<tr><td><a href="https://pubmed.ncbi.nlm.nih.gov/27831498/" target="_blank">27831498</a></td><td>Inoue et al.</td><td>2017</td><td>Shendure Lab</td><td>HepG2</td><td>lentiMPRA</td><td>2,241</td></tr> +<tr><td><a href="https://pubmed.ncbi.nlm.nih.gov/30045748/" target="_blank">30045748</a></td><td>Klein et al.</td><td>2018</td><td>Shendure Lab</td><td>HepG2</td><td>STARR-seq</td><td>7,064</td></tr> +<tr><td><a href="https://pubmed.ncbi.nlm.nih.gov/32483191/" target="_blank">32483191</a></td><td>Choi et al.</td><td>2020</td><td>Brown Lab</td><td>HEK293FT</td><td>lentiMPRA</td><td>840</td></tr> +<tr><td><a href="https://pubmed.ncbi.nlm.nih.gov/32483191/" target="_blank">32483191</a></td><td>Choi et al.</td><td>2020</td><td>Brown Lab</td><td>UACC903</td><td>lentiMPRA</td><td>840</td></tr> +<tr><td><a href="https://pubmed.ncbi.nlm.nih.gov/32819422/" target="_blank">32819422</a></td><td>Mattioli et al.</td><td>2020</td><td>Mele Lab</td><td>HUES64</td><td>plasmidMPRA</td><td>6,954</td></tr> +<tr><td><a href="https://pubmed.ncbi.nlm.nih.gov/32819422/" target="_blank">32819422</a></td><td>Mattioli et al.</td><td>2020</td><td>Mele Lab</td><td>mESC</td><td>plasmidMPRA</td><td>6,954</td></tr> +<tr><td><a href="https://pubmed.ncbi.nlm.nih.gov/33046894/" target="_blank">33046894</a></td><td>Klein et al.</td><td>2020</td><td>Shendure Lab</td><td>HepG2</td><td>lentiMPRA</td><td>8,116</td></tr> +<tr><td><a href="https://pubmed.ncbi.nlm.nih.gov/33046894/" target="_blank">33046894</a></td><td>Klein et al.</td><td>2020</td><td>Shendure Lab</td><td>HepG2</td><td>plasmidMPRA</td><td>2,228</td></tr> +<tr><td><a href="https://pubmed.ncbi.nlm.nih.gov/33046894/" target="_blank">33046894</a></td><td>Klein et al.</td><td>2020</td><td>Shendure Lab</td><td>HepG2</td><td>STARR-seq</td><td>2,230</td></tr> +<tr><td><a href="https://pubmed.ncbi.nlm.nih.gov/36834916/" target="_blank">36834916</a></td><td>Koesterich et al.</td><td>2023</td><td>Kreimer Lab</td><td>NPC</td><td>lentiMPRA</td><td>3,807</td></tr> +</table> + +<h2>Data Access</h2> +<p> +The data can be explored interactively in table format with the +<a href="../cgi-bin/hgTables">Table Browser</a> or the +<a href="../cgi-bin/hgIntegrator">Data Integrator</a> +and exported from there to spreadsheet or tab-sep tables. +From scripts, the data can be accessed through our +<a href="https://api.genome.ucsc.edu" target="_blank">API</a>, track=<i>mprabase</i>. +</p> +<p> +For automated download and analysis, the genome annotation is stored in a bigBed +file that can be downloaded from +<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/mpra/mprabase" target="_blank">our download server</a>. +The file for this track is called <tt>mprabase.bb</tt>. Individual +regions or the whole genome annotation can be obtained using our tool +<tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a +precompiled binary for your system. Instructions for downloading source code and +binaries can be found +<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. +The tool can also be used to obtain features within a given range, e.g. +<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/mpra/mprabase/mprabase.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt> +</p> +<p> +The original data can be downloaded from the +<a href="http://mprabase.ucsf.edu/app/mprabase" target="_blank">MPRA Base web application</a>. +</p> + +<h2>Credits</h2> +<p> +Thanks to Varda Singhal, Jianyu Zhao, and the +<a href="https://pharm.ucsf.edu/ahituv" target="_blank">Ahituv Lab</a> +at the University of California San Francisco for creating and curating MPRA Base and for creating this track. +</p> + +<h2>References</h2> + + +<p> +Zhao J, Baltoumas FA, Konnaris MA, Mouratidis I, Liu Z, Sims J, Agarwal V, Pavlopoulos GA, +Georgakopoulos-Soares I, Ahituv N. +<a href="https://doi.org/10.1101/2023.11.19.567742" target="_blank"> +MPRAbase: A Massively Parallel Reporter Assay Database</a>. +<em>bioRxiv</em>. 2023 Nov 22;. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/38045264" target="_blank">38045264</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10690217/" target="_blank">PMC10690217</a> +</p> +