a57e95fd50c67dfcb633c5732844d411655b07a0 jnavarr5 Fri Oct 24 15:46:37 2025 -0700 Fixing a singular-plural disconnect that Bob wrote in about, refs #36576 diff --git src/hg/makeDb/trackDb/human/hg38/mane.html src/hg/makeDb/trackDb/human/hg38/mane.html index 5db45b22a90..dbe44761652 100644 --- src/hg/makeDb/trackDb/human/hg38/mane.html +++ src/hg/makeDb/trackDb/human/hg38/mane.html @@ -1,68 +1,70 @@ <h2>Description</h2> <p> The <a href="https://www.ncbi.nlm.nih.gov/refseq/MANE/" target="_blank">Matched Annotation from NCBI and EMBL-EBI (MANE)</a> project aims to produce a matched set of high-confidence transcripts that are identically annotated between RefSeq (NCBI) and Ensembl/GENCODE (led by EMBL-EBI). Transcripts for MANE are chosen by a combination of automated and manual methods based on conservation, expression levels, clinical significance, and other factors. Transcripts are matched between the NCBI RefSeq and Ensembl/GENCODE annotations based on the GRCh38 genome assembly, with precise 5' and 3' ends defined by high-throughput sequencing or other available data.</p> -<p>This track is automatically updated, see the <b>source data version</b> above for the current version -number. MANE include almost all human protein-coding genes and genes of clinical relevance, including genes in the +<p> +This track is automatically updated, see the <b>source data version</b> above for the current +version number. MANE includes almost all human protein-coding genes and genes of clinical relevance, +including genes in the <a href="https://www.acmg.net/PDFLibrary/41436_2021_1172_OnlinePDF-1.pdf" target="_blank">American College of Medical Genetics and Genomics (ACMG) Secondary Findings list (SF) v3.0</a>. It includes both <b>MANE Select</b> and <b>MANE Plus Clinical</b> transcripts. <b>MANE Plus Clinical</b> items are <b><font color=red>colored red</font></b>. <p> For more information on the different gene tracks, including MANE vs GENCODE or RefSeq, see our <a href="/FAQ/FAQgenes.html#ens" target="_blank">Genes FAQ</a>.</p> <h2>Data Access</h2> <p> The raw data can be explored interactively with the <a href="../cgi-bin/hgTables" target="_blank">Table Browser</a>, or the <a href="../cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>. For computational analysis, genome annotations are stored in a bigGenePred file that can be downloaded from the <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/mane/" target="_blank">download server</a>. Regional or genome-wide annotations can be converted from binary data to human readable text using our command line utility <em>bigBedToBed</em> which can be compiled from source code or downloaded as a precompiled binary for your system. Files and instructions can be found in the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">utilities directory</a>. The utility can be used to obtain features within a given range, for example:</p> <code>bigBedToBed -chrom=chr6 -start=0 -end=1000000 http://hgdownload.soe.ucsc.edu/gbdb/hg38/mane/mane.bb stdout</code> <p> Download links for MANE: <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/MANE">ftp://ftp.ncbi.nlm.nih.gov/refseq/MANE</a> </p> <p> Previous MANE versions are also available on our <a href="https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg38/mane/" target="_blank">download archive</a>.</p> <p> Please refer to our <a href="../FAQ/FAQdownloads.html#download36" target="_blank">Data Access FAQ</a> for more information or our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" target="_blank">mailing list</a> for archived user questions.</p> <h2>Credits</h2> <p> Thank you to the RefSeq project at NCBI and the Ensembl/GENCODE project at EMBL-EBI. You can contact the authors directly at <A HREF="mailto:MANE-help@ncbi. nlm.nih.gov"> MANE-help@ncbi.nlm.nih.gov</A> or <A HREF="mailto:mane-help@ebi.ac.uk"> mane-help@ebi.ac.uk</A>.</p> <h2>References</h2> <p> Morales J, Pujar S, Loveland JE, Astashyn A, Bennett R, Berry A, Cox E, Davidson C, Ermolaeva O, Farrell CM <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/35388217" target="_blank"> A joint NCBI and EMBL-EBI transcript set for clinical genomics and research</a>. <em>Nature</em>. 2022 Apr;604(7905):310-315. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35388217" target="_blank">35388217</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007741/" target="_blank">PMC9007741</a> </p>