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 @@ -1,127 +1,152 @@ <!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>