64bd5703470f683544d89164884fe40ec30b71bc gperez2 Thu Feb 6 16:45:59 2025 -0800 Added more details to spliceImpactSuper.html and added a SpliceVarDB link on the hgc page, refs #34424 diff --git src/hg/makeDb/trackDb/human/spliceImpactSuper.html src/hg/makeDb/trackDb/human/spliceImpactSuper.html index 601d4be02bb..242e7284c6b 100644 --- src/hg/makeDb/trackDb/human/spliceImpactSuper.html +++ src/hg/makeDb/trackDb/human/spliceImpactSuper.html @@ -1,42 +1,68 @@ <h2>Description</h2> <p> The "Splicing Impact" container track contains tracks showing the predicted or validated effect of variants close to splice sites. </p> <h3>SpliceVarDB</h3> <p>SpliceVarDB is an online database consolidating over 50,000 variants assayed for their effects on splicing in over 8,000 human genes. The authors evaluated over 500 published data sources and established a spliceogenicity scale to standardize, harmonize, and consolidate variant validation data generated by a -range of experimental protocols. The database is available at +range of experimental protocols. Genes and variant locations were obtained using +GENCODE v44. Splice regions were calculated as specific distances from the closest +canonical exon, including 5' and 3' untranslated regions (UTRs). The +database is available at <a target=_blank href="https://splicevardb.org">splicevardb.org</a>.</p> <h2>Display Conventions and Configuration</h2> <h3>SpliceVarDB</h3> <p>According to the strength of their supporting -evidence, variants were classified as "splice-altering" (∼25%), "not -splice-altering" (∼25%), and "low-frequency splice-altering" (∼50%), which +evidence, variants were classified as "splice-altering" (~25%), "not +splice-altering" (~25%), and "low-frequency splice-altering" (~50%), which correspond to weak or indeterminate evidence of spliceogenicity. 55% of the splice-altering variants in SpliceVarDB are outside the canonical splice sites (5.6% are deep intronic). The data is shown as lollipop plots that can be clicked, the details page then shows a link to SpliceVarDb with full details. </p> +<p>The classification thresholds primarily follow those established by the original study. +However, most studies only defined criteria for splice-altering variants and did not define +criteria for variants that resulted in normal splicing. The authors implemented stringent +thresholds to define the normal category and ensure a high-quality set of control variants. +Variants that did not meet these criteria were classified as low-frequency splice-altering +variants with a wide range of sub-optimal scores. Variants that fell between the normal and +splice-altering classifications were placed into a low-frequency splice-altering category. +In situations where a variant was validated multiple times, if at least one validation +returned splice-altering and another returned normal, the "conflicting" category +was applied. +</p> + +<P> +The lollipop plots are color-coded based on the <b>score</b> value, which corresponds +to the following classifications: +<ul> + <li><b>3</b> - <span style="color: rgb(219,61,61);">Splice-altering</span></li> + <li><b>2</b> - <span style="color: rgb(128,82,160);">Low-frequency</span></li> + <li><b>1</b> - <span style="color: rgb(57,135,204);">Normal</span></li> + <li><b>0</b> - <span style="color: rgb(140,140,140);">Conflicting</span></li> +</ul> +</P> + <h2>Data Access</h2> <p> The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. The data can be accessed from scripts through our <a href="https://api.genome.ucsc.edu">API</a>, the track name is "splicevardb". <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/$db/splicevardb/" target="_blank">our download server</a>. The file for this track is called <tt>SVADB.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