3df056201a1057053451c8ea38cb72419f3e75a1 max Wed Mar 20 11:13:48 2019 +0100 genes faq page intro change, #22696 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 0a1fc49..8a7151d 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -1,327 +1,352 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser FAQ" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Frequently Asked Questions: Gene tracks</h1> <h2>Topics</h2> <ul> <li><a href="#gene">What is a gene?</a></li> -<li><a href="#genestrans">What is the difference between a gene and a transcript?</a></li> +<li><a href="#genestrans">What is a transcript and how is it related to a gene?</a></li> <li><a href="#mostCommon">What are the most common gene transcript tracks?</a></li> <li><a href="#genename">What is a gene name?</a></li> <li><a href="#ens">What are Ensembl and GENCODE and is there a difference?</a></li> <li><a href="#ensRefseq">What are the differences among GENCODE, Ensembl and RefSeq?</a></li> <li><a href="#hg19">For the human assembly hg19/GRCh37: What is the difference between "UCSC Genes" track, the "GENCODE" track and the "Ensembl Genes" track?</a></li> <li><a href="#hg38">For the human assembly hg38/GRCh38: What are the differences between the "GENCODE" and "All GENCODE" tracks?</a></li> <li><a href="#gencode">What is the difference between GENCODE comprehensive and basic?</a></li> <li><a href="#ncbiRefseq">What is the difference between "NCBI RefSeq" and "UCSC RefSeq"?</a></li> <li><a href="#ccds">What is CCDS?</a></li> <li><a href="#justsingle">How can I just show a single transcript per gene?</a></li> <li><a href="#whatdo">This is rather complicated. Can you tell me which gene transcript track I should use?</a></li> </ul> <hr> <p> <a href="index.html">Return to FAQ Table of Contents</a></p> <a name="gene"></a> <h2>The basics</h2> + +The genome browser contains many gene annotation tracks. Our users +often wonder what these contain and where the information that we present comes +from. + <h6>What is a gene?</h6> <p> -Before DNA sequencing, genes were defined as heritable traits. In the present day context of -bioinformatics, a gene represents a collection of transcripts usually transcribed within certain -genomic coordinates. Transcripts either encode one protein or are non-coding. -For human, most genes have an associated symbol assigned by the <a target=_blank -href="https://www.genenames.org/">Human Gene Nomenclature Committee (HGNC, formerly HUGO)</a>. -For other organisms there is usually a database curation -team that assigns symbols, such as MGI for mouse. +The exact definition of "gene" depends on the context. In the context of +genome annotation, a gene has at least a name and is defined by a collection of +related mRNA transcript sequences ("isoforms"). The naming of genes and the +assignment of the most important transcript sequences is often done manually by +a group of biological literature curators. For human, genes names are created +by the <a target=_blank href="https://www.genenames.org/">Human Gene +Nomenclature Committee (HGNC, formerly HUGO)</a>. Non-human species have +similar annotation groups, e.g. Mouse Genome Informatics, Wormbase, Flybase, +etc. </p> <a name="genestrans"></a> -<h6>What is the difference between a gene and a transcript? </h6> +<h6>What is a transcript and how is it related to a gene? </h6> <p> -Transcripts are defined as RNA molecules that are copied from the DNA template of a gene. Every -gene is comprised of a set of transcripts. In the Genome Browser, data tracks are often called +Transcripts are defined as RNA molecules that are made from a DNA template. +Databases like the ones at the National Library of Medicine's NCBI or the +European Bioinformatics Institute (EBI) collect these transcript sequences from +biologists working on a gene. Every transcript has a +unique identifier (accession), a gene that it is assigned to, a sequence, and +a list of exon chrom/start/end coordinates on a chromosome. +Usually every transcript is assigned to only a single gene. In the Genome Browser, transcript +tracks often end with the word "Genes", e.g. "Ensembl Genes", "NCBI RefSeq Genes" or "UCSC -Genes", but they really represent transcripts on an assembly. Every transcript has an -accession number, a sequence, and a list of exon chrom/start/end coordinates on a genome assembly. -These transcript accession numbers are assigned to genes. </p> +Genes", but they really represent transcripts on chromosomes of a genome assembly.</p> <p> -For example, the gene with the gene symbol <a target=_blank -href="https://www.ncbi.nlm.nih.gov/gene/672#">BRCA1</a> has 5 protein-coding transcripts -or isoforms. The first transcript has the NCBI accession number <a target=_blank -href="https://www.ncbi.nlm.nih.gov/nuccore/NM_007294.3">NM_007294.3</a> which produces -the protein <a target=_blank href="https://www.ncbi.nlm.nih.gov/protein/NP_009225.1"> -NP_009225.1</a>. This transcript is comprised of <a target=_blank -href="https://www.ncbi.nlm.nih.gov/nuccore/U14680">23 exons</a>.</p> +For example, using the databases by NCBI, the gene +with the gene symbol <a target=_blank +href="https://www.ncbi.nlm.nih.gov/gene/672#">BRCA1</a> has 5 protein-coding +transcripts or isoforms. The first transcript has the NCBI accession number <a +target=_blank +href="https://www.ncbi.nlm.nih.gov/nuccore/NM_007294.3">NM_007294.3</a> which +produces the protein with the accession<a target=_blank +href="https://www.ncbi.nlm.nih.gov/protein/NP_009225.1"> NP_009225.1</a>. In +the human genome, it is located on chromosome 17, where it is comprised of <a +target=_blank href="https://www.ncbi.nlm.nih.gov/nuccore/U14680">23 exons</a>. +On the version GRCh38 of the human genome, these exons cover the DNA +nucleotides 43044295 to 43125483.</p> <a name="mostCommon"></a> <h6>What are the most common gene transcript tracks?</h6> <p> -Originally, researchers sequenced cDNA and submitted the sequences to Genbank. The +Researchers sequence cDNA sequences and send these to NCBI Genbank. The Genome Browser shows these sequences in the Genbank or the <a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=est">EST track</a> (if the cDNA is just a single read from the 5' or 3' end). From the alignment of the cDNAs and ESTs, the NCBI RefSeq group manually creates a smaller set of representative transcripts which we display as the <a target=_blank href=../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite>RefSeq Curated</a> track. Automated programs like UCSC's or Ensembl's gene build software do the same, just in software, which is more systematic but also more error-prone. With the arrival of GENCODE, Ensembl added a manual curation to their -human and mouse transcripts. NCBI has since also added an automated predictions pipeline with -their tool Gnomon and its resulting "<a target=_blank -href=../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite>RefSeq Predicted</a>" transcripts.</p> +human and mouse transcripts. NCBI has added an automated prediction software (Gnomon) +which we show in the "<a target=_blank +href=../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite>RefSeq Predicted</a>" track.</p> <p>There are many other tracks in the group "Genes and Gene Predictions". <a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=genscan">Genscan</a> and <a target=_blank href="../cgi-bin/hgTrackUi?db=hg19&g=nscanGene">N-Scan</a> are older transcript predictor algorithms that are based on the genome sequence alone. <a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=augustusGene">Augustus</a> and <a target=_blank href="../cgi-bin/hgTrackUi?db=hg19&g=acembly">AceView</a> are automated gene-predictors that use cDNA and EST data. These and similar gene tracks are only relevant when you are working on a particular locus where you think that the manually curated gene models (Ensembl and RefSeq) have errors.</p> <a name="genename"></a> -<h6>What is a gene name? </h6> +<h6>What is a gene or transcript accession? </h6> <p> -The most common gene names (sometimes called accession numbers) encountered by users -are either from Ensembl, GENCODE, RefSeq, or -gene symbols. For gene symbols, such as DDX11L1, see the above question <a -href="FAQgenes.html#gene">"What is a gene?"</a>. Ensembl/GENCODE transcript accession numbers in -the human genome start with ENST followed by a number, e.g. "ENST00000619216.1". Every -transcript is assigned to a gene with identifiers that start with ENSG and every ENSG has at least -one ENST assigned to it. Manually curated RefSeq transcript identifiers start with -NM_ (coding) or NR_ (non-coding), followed by a number, or XM_ if they are predicted by -software, e.g. "NR_046018.2". A table of all RefSeq prefixes can be found on the <a -target=_blank href= -"https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/?report=objectonly"> +Gene symbols like BRCA1 are easy to remember but sometimes change and are not +specific to an organism. Therefore most databases internally use unique +identifiers to refer to sequences and some journals require authors to use +these in manuscripts.<br> + +The most common accession numbers encountered by users are either from Ensembl, +GENCODE or RefSeq. Human Ensembl/GENCODE gene accession numbers start with +ENSG, e.g. "ENSG00000012048" for BRCA1. Every ENSG-gene has at least +one transcript assigned to it. The transcript identifiers start with with ENST +followed by a number, e.g. "ENST00000619216.1". NCBI refers to genes +with plain numbers, e.g. 672 for BRCA1. Manually curated RefSeq transcript +identifiers start with NM_ (coding) or NR_ (non-coding), followed by a number and version +number separated by a dot, e.g. "NR_046018.2". If the transcript was +predicted by the NCBI Gnomon software, the prefix is XM_ but these are rare in human. +A table of these and other RefSeq prefixes can be +found on the <a target=_blank +href="https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/?report=objectonly"> NCBI website</a>. </p> <a name="ens"></a> <h2>The differences</h2> + +Some of our gene tracks look similar and contain very similar information which can be confusing. + <h6>What are Ensembl and GENCODE and is there a difference?</h6> <p> Officially, the Ensembl and GENCODE gene models are the same. On the latest human and mouse genome assemblies (hg38 and mm10), the identifiers, transcript sequences, and exon coordinates are almost identical between equivalent Ensembl and GENCODE versions (excluding <a target=_blank href="FAQdownloads.html#downloadAlt">alternative sequences</a> or <a target=_blank href="FAQdownloads.html#downloadFix">fix sequences</a>).</p> <p>GENCODE uses the UCSC convention of prefixing chromosome names with "chr", e.g. "chr1" and "chrM", but Ensembl calls these "1" or "MT". At the time of writing (Ensembl 89), a few transcripts differ due to conversion issues. In addition, around 160 PAR genes are duplicated in GENCODE but only once in Ensembl. The differences affect fewer than 1% of the transcripts. Apart from gene annotation itself, the links to external databases differ.</p> <p>The <a target=_blank href="https://www.gencodegenes.org/human/releases.html">GENCODE Release History</a> shows the release dates and can be linked to corresponding Ensembl releases. You can download the gene transcript models from the website <a target=_blank href=https://gencodegenes.org>https://gencodegenes.org</a> or from <a target=_blank href=http://ensembl.org>http://ensembl.org</a>. For most applications, the files distributed on the GENCODE website should be easier to use, as the third party database links are easier to parse and the sequence identifiers match the UCSC genome files, at least for the primary chromosomes.</p> <p> Additional information on this question can be found on the <a target=_blank href= "https://www.gencodegenes.org/pages/faq.html">GENCODE FAQ page</a>.</p> <a name="ensRefseq"></a> <h6>What are the differences among Ensembl, GENCODE and RefSeq?</h6> <p> Different institutions have different rules on how they annotate genes. E.g. RefSeq's criteria are more stringent, so there are fewer RefSeq transcripts than Ensembl/GENCODE transcripts. Also, RefSeq transcripts have their own sequences independent of the genome assembly, so certain population-specific variants may be in RefSeq that are entirely missing from the reference genome sequence. This has the important implication that the position of genome variants are harder to map to RefSeq transcripts than for GENCODE since RefSeq transcripts can have additional sequence or missing sequence relative to the genome.</p> <p>The links from either transcript model to other gene-related databases are different. In general, it seems that high-throughput sequencing data results, e.g. RNA-seq, are often using Ensembl/GENCODE annotations and human genetics results are reported using RefSeq annotations. It depends on your particular project which gene model set you want to use. Over time, the two transcript databases have been and are becoming more similar. <a name="hg19"></a> <h6>For the human assembly hg19/GRCh37: What is the difference between UCSC Genes, the "GENCODE Gene Annotation" track and the "Ensembl Genes" track?</h6> <p>The "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg19&g=knownGene">UCSC Genes</a>" track, also called "Known Genes", is available only on assemblies before hg38. It was built with a gene predictor developed at UCSC. This gene predictor uses protein, EST and cDNA annotations to derive a relatively restricted gene transcript set. The software is no longer in use and there are no plans to release the track on newer human assemblies. It was last used for the mm10 mouse assembly. We are considering updating the hg19 annotation produced by this software and are interested in any user feedback on the topic.</p> <p>The "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeSuper">GENCODE Gene Annotation</a>" track contains data from all versions of GENCODE. "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg19&g=ensGene">Ensembl Genes</a>" track contains just a single Ensembl version. See the previous question for the differences between Ensembl and GENCODE. </p> <a name="hg38"></a> <h6>For the human assembly hg38/GRCh38: What are the differences between the "GENCODE" and "All GENCODE" tracks?</h6> <p> "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=knownGene">GENCODE</a>" is the default gene track on hg38 (similar to "Known Genes" on hg19), which means that it is associated with a large amount of third party information when you click on a gene. This related information is also available using the Table Browser. This GENCODE track is updated periodically to match the latest GENCODE release. "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeSuper">All GENCODE</a>" is a super-track that contains all versions of GENCODE as sub-tracks, but these tracks have less third-party information. Sub-tracks are never removed from "All GENCODE", and new sub-tracks are added as there are additional GENCODE releases. </p> <a name="gencode"></a> <h6>What is the difference between "GENCODE Comprehensive" and "GENCODE Basic"?</h6> <p> The "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=knownGene">GENCODE</a>" track offers a "basic" gene set, and a "comprehensive" gene set. The "basic" gene set represents a subset of transcripts that GENCODE believes will be useful to the majority of users. The "basic" gene set is defined as follows in the <a target=_blank href="https://www.gencodegenes.org/pages/tags.html">GENCODE FAQ</a>:</p> <p><i> "Identifies a subset of representative transcripts for each gene; prioritises full-length protein coding transcripts over partial or non-protein coding transcripts within the same gene, and intends to highlight those transcripts that will be useful to the majority of users."</i></p> <p> By default, the track displays only the "basic" set. In order to display the complete "comprehensive" set, the box can be ticked at the top of the <a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=knownGene">GENCODE track description page</a>.</p> <p class='text-center'> <img class='text-center' src="../images/ComprehensiveSet.png" alt="Turning on comprehensive gene set" width="750"> <a name="ncbiRefseq"></a> <h6>What is the difference between "NCBI RefSeq" and "UCSC RefSeq"?</h6> <p> RefSeq gene transcripts, unlike GENCODE/Ensembl/UCSC Genes, are sequences that can differ from the genome. They need to be aligned to the genome to create transcript models. Traditionally, UCSC has aligned RefSeq with BLAT (UCSC RefSeq sub-track) and NCBI has aligned with splign. The advantages of the UCSC alignments are that they are updated more frequently and are available for older assemblies (like GRCh37/hg19), but they are less stable and they are not the official alignments. Therefore we recommend working with the NCBI annotations. When an assembly has an "NCBI RefSeq" track, we show it by default and hide the "UCSC RefSeq" track. </p> <p> In some rare cases, the NCBI and UCSC exon boundaries differ. Activating both RefSeq and UCSC RefSeq tracks helps you investigate the differences. Activating the RefSeq Alignments track shows NCBI's splign alignments in more detail, including double lines where both transcript and genomic sequence are skipped in the alignment. When available, the RefSeq Diffs subtrack may be helpful too. The upcoming <a target=_blank href=https://ncbiinsights.ncbi.nlm.nih.gov/2018/10/11/matched-annotation-by-ncbi-and-embl-ebi-mane-a-new-joint-venture-to-define-a-set-of-representative-transcripts-for-human-protein-coding-genes/>MANE gene set</a> will contain a set of high-quality transcripts that are 100% alignable to the genome and are part of both RefSeq and Ensembl/GENCODE but at the time of writing this project is at an early stage. </p> <p> An anecdotal and rare example is SHANK2 and SHANK3 in hg19. It is impossible for either NCBI or BLAT to get the correct alignment and gene model because the genome sequence is missing for part of the gene. NCBI and BLAT find slightly different exon boundaries at the edge of the problematic region. NCBI's aligner tries very hard to find exons that align to any transcript sequence, so it calls a few small dubious "exons" in the affected genomic region. GENCODE V19 also used an aligner that tried very hard to find exons, but it found small dubious "exons" in different places than NCBI. The <a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite">RefSeq Alignments</a> subtrack makes the problematic region very clear with double lines indicating unalignable transcript sequence. </p> <p> When reporting results as RefSeq coordinates, e.g. as HGVS, in research articles, please specify the RefSeq annotation release and also the RefSeq transcript ID with version (e.g. NM_012309.4 not NM_012309). Different RefSeq transcript versions have different sequence (for example, more sequence may be added to the UTRs or even the CDS), and so the transcript coordinates often change from one version to the next. </p> <a name="ccds"></a> <h6>What is CCDS?</h6> <p> The <a target=_blank href="https://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi"> Consensus Coding Sequence Project</a> is a list of transcript coding sequence (CDS) genomic regions that are identically annotated by RefSeq and Ensembl/GENCODE. CCDS undergoes extensive manual review and you can consider these a subset of either gene track, filtered for high quality. The CCDS identifiers are very stable and allow you to link easily between the different databases. As the name implies, it does not cover UTR regions or non-coding transcripts. </p> <a name="justsingle"></a> <h6>How can I just show a single transcript per gene?</h6> <p> For the tracks "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg19&g=knownGene">UCSC Genes</a>" (hg19) or "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=knownGene">GENCODE Genes</a>" (hg38), click on their title and on the configuration page, uncheck the box "Show splice variants". Only a single transcript will be shown. The method for how this transcript is selected is described in the track documentation below the configuration settings.</p> <p class='text-center'> <img class='text-center' src="../images/SpliceVariants.png" alt="Changing splice variants" width="750"> <p>For the track <a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite"> NCBI RefSeq</a> (hg38), you can activate the subtrack "RefSeq HGMD". It contains only the transcripts that are part of the Human Gene Mutation Database. </p> <a name="whatdo"></a> <h6>This is rather complicated. Can you tell me which gene transcript track I should use?</h6> <p> For automated analysis, if you are doing NGS analysis and you need to capture all possible transcripts, GENCODE provides a comprehensive gene set. For human genetics or variant annotation, a more restricted transcript set is usually sufficient and "NCBI RefSeq" is the standard. If you are only interested in protein-coding annotations, CCDS or UniProt may be an option, but this is rather unusual. </p> <p> For manual inspection of exon boundaries of a single gene, and especially if it is a transcript that is repetitive or hard to align (e.g. very small exons), look at the UCSC RefSeq track and watch for differences between the NCBI and UCSC exon placement. You can also BLAT the transcript sequence. Manually look at ESTs, mRNAs, TransMap and possibly Augustus, Genscan, SIB, SGP or GeneId in obscure cases where you are looking for hints on what an alternative splicing could look like.</p> <p> You may also find the <a target="_blank" href="http://genome.ucsc.edu/s/view/GeneSupport">Gene Support</a> public session helpful. This session is a collection of tracks centered around supporting evidence for genes.</p> </p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->