9861b0b8447a0433000fb3e35cf652b01d1672d1 brianlee Fri Mar 4 12:13:36 2022 -0800 Incorporating MarkDs input on non-coding GENCODE, noting how lncRNA miRNA pseudogenes are not an unambiguous topic refs #29030 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index a30ec1e..886c96d 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -613,60 +613,82 @@ href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/">hg38 GTF files</a>.</p> <a name="coding"></a> <h2>What is the best way to get only coding genes (or only non-coding genes) out of GENCODE (or other gene) tables?</h2> <h3>Coding genes</h3> <p> One option for GENCODE is to use the Public MySQL server and the following query: <pre> mysql --user=genome --host=genome-mysql.soe.ucsc.edu -Ne 'select * from wgEncodeGencodeBasicV39 where cdsStartStat = "cmpl" and cdsEndStat = "cmpl";' hg38 </pre></p> <p> What this query does is access the hg38 database, and then from the wgEncodeGencodeBasicV39 table, looks to the fields of cdsStartStat and cdsEndStat for only those entries with the value cmpl, showing "CDS is complete" at the start and end, so that these are genes that are -protein-coding entries, thereby excluding non-coding RNA genes.</p> +protein-coding entries, thereby excluding non-coding RNA genes. Please note that this query +will return genes one may not want (or want), such as Immunoglobulin and T-cell receptor components.</p> <p> For the manually curated RefSeq gene set transcript identifiers start with NM_ for coding or NR_ for non-coding, followed by a number and version number separated by a dot, e.g. "NR_046018.2" for an RNA pseudogene. For RefSeq one can select coding genes by -filtering for NM identifiers.</p> +filtering for NM identifiers. On the concept of genes, it may be worth noting that the +NR_046018.2 example is a transcribed pseudogene of an mRNA. So it is considered an RNA, +and by many a lncRNA (long non-coding RNA), where the whole idea of transcribed pseudogenes +is not an unambiguous concept to a lot of biologists. For some, another example, "NR_106918.1" +represents a miRNA (microRNA), which are short (20-24 nt) non-coding RNAs, may provide a +more familiar idea of the kind of non-coding elements desired to be removed. +</p> <p>If using the UCSC knownGene table one can filter for where the coding start and coding end fields of the table are not equivalent, e.g. <code>knownGene.cdsStart != knownGene.cdsEnd</code>, which would ensure the selected entries are coding genes.</p> <p> You can also <a href="https://groups.google.com/u/1/a/soe.ucsc.edu/g/genome/search?q=only%20coding%20genes" target="_blank">search our mailing-list archives</a> to read further details about only obtaining coding genes from the UCSC Genome Browser.</p> <a name="nonCoding"></a> <h3>Non-coding genes</h3> <p> -The steps for selecting non-coding genes are essentially the opposite of the steps to select -only coding genes. One option for GENCODE is to use the Public MySQL server -and the following query:</p> +The steps for selecting non-coding genes are not exactly the opposite of the steps to select +only coding genes. The above discussion introduced the idea of lncRNA (long non-coding RNA) +and miRNA (microRNA), hinting at the abundant types of RNA molecules.</p> +<p> +Since there are many different kinds of non-coding elements in GENCODE, a better step for non-coding +selection is to join data with a related attributes table, and specifically name a desired biotype or biotypes.</p> +<p> +Here is an introductory example using the Public MySQL server to access the wgEncodeGencodeBasicV39 table of all genes +and the wgEncodeGencodeAttrsV39 related table to find the transcriptType for each entry and simply to select not +protein-coding genes. There are a number of biotypes that can be accessed by looking at the table scheme +and clicking the values link for the +<a href="http://genome.ucsc.edu/cgi-bin/hgTables?hgta_database=hg38&hgta_histoTable=wgEncodeGencodeAttrsV39&hgta_doValueHistogram=transcriptType" +target="_blank">transcriptType</a> field. The below example will attempt to make a simple example to select +all types that do not have "protein_coding" in this field:</p> <p> <pre> - mysql --user=genome --host=genome-mysql.soe.ucsc.edu -Ne 'select * from wgEncodeGencodeBasicV39 where cdsStartStat != "cmpl" and cdsEndStat != "cmpl";' hg38 +hgsql hg38 -e 'select g.name,a.transcriptType from wgEncodeGencodeBasicV39 g, wgEncodeGencodeAttrsV39 a where (g.name = a.transcriptId) and (a.transcriptType != "protein_coding") order by g.name;' </pre></p> <p> What this query does is access the hg38 database, and then from the wgEncodeGencodeBasicV39 table, -looks to the fields of cdsStartStat and cdsEndStat for only those entries without the value cmpl, -showing "CDS is complete" at the start and end, so that this removes genes that are -protein-coding entries, thereby selecting only non-coding RNA genes.</p> +it takes the name field (g.name) and looks in the related wgEncodeGencodeAttrsV39 table for a matching +transcriptId field (g.name = a.transcriptId), and then screens for only entries in wgEncodeGencodeAttrsV39 +that are not equal to protein-coding (a.transcriptType != "protein_coding"). In this way selecting all the +many types, which again may not be the entire subset desired. By modifying the above query it is possible +to add further qualifiers and refine the subset of non-coding elements desired.</p> <p> For the manually curated RefSeq gene set transcript identifiers start with NM_ for coding or NR_ for non-coding, followed by a number and version number separated by a dot, e.g. "NR_046018.2" for an RNA pseudogene. For RefSeq, one can select non-coding genes by -filtering for NR identifiers.</p> -<p>If using the UCSC knownGene table one can filter for where the coding start +filtering for NR identifiers. Note that a pseudogene of mRNA is not an unambiguous concept, +and there may be a desire to look further to select certain subset types as mentioned above.</p> +<p> +If using the UCSC knownGene table one can filter for where the coding start and coding end fields of the table are equivalent, e.g. <code>knownGene.cdsStart = knownGene.cdsEnd</code>, which would ensure the selected entries are non-coding genes.</p> <p> You can also <a href="https://groups.google.com/u/1/a/soe.ucsc.edu/g/genome/search?q=only%20non-coding%20genes" target="_blank">search our mailing-list archives</a> to read further details about only obtaining non-coding genes from the UCSC Genome Browser.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->