Hi,
I am trying to generate a BED file following the below steps:
Go to human hg19 UCSC Table Browser:
track: UCSC Genes
table: knownCanonical
output format: select fields from primary and related tables
press get output
select fields from hg19.knownCanonical: chrom, chromStart, chromEnd,transcript
select fields from hg19.kgXref: geneSymbol
press get output
This BED file does not have the gene BBS5 in it. I am sure that this gene do exist
However, when I follow the same steps except selecting the table = knownGenes (instead of knownCanonical) , I can see BBS5 gene. The question is why this gene does not appear in the table knownCanonical?
Any insights?
1 answer
Hello Vijay,
What you are observing here with the missing BBS5 entry in the knownCanonical table is an artifact of how that table was created for hg19. If you take a look at the hg19 UCSC Genes description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene ) we define knownCanonical as the following:
knownCanonical identifies the canonical isoform of each cluster ID, or gene. Generally, this is the longest isoform.
The problem is, however, when two genes have overlapping coordinates, and one of them is entirely within another, the algorithm considers them isoforms and the smaller gene will be missed by knownCanonical. You can see this with BBS5 by going to the following session (http://genome.ucsc.edu/s/Lou/hg19_MLQ1 ). KLHL41 has a transcript with the same start site as BBS5, however, it extends much further. All of the BBS5 transcripts fall within it. If you query the Table Browser for these coordinates you see only KLHL41.
Using coordinates chr2:170,331,250-170,374,046:
chr2 170366211 170382772 17243 uc002ueu.1 uc002ueu.1 KLHL41
In order to get around this, you can use the complete knownGenes table, or you could also use the knownCanonical table for hg38. For the hg38 assembly (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene ) the table was generated differently:
knownCanonical identifies the canonical isoform of each cluster ID or gene using the ENSEMBL gene IDs to define each cluster. The canonical transcript is chosen using the APPRIS principal transcript when available. If no APPRIS tag exists for any transcript associated with the cluster, then a transcript in the BASIC set is chosen. If no BASIC transcript exists, then the longest isoform is used.
This new method did not have the same issue as hg19, as it uses APPRIS tags, then GENCODE sets, and then finally if those are not available the longest isoform. If you convert the region from the session above to hg38 (View in the top bluebar -> In Other Genomes) you will get the following coordinates (chr2:169,474,740-169,517,536), then if you query the position on the knownCanonical table on the Table Browser you get the following results:
chr2 169479177 169506655 10932 ENST00000295240.7 ENSG00000163093.11 BBS5
chr2 169479479 169525922 41682 ENST00000513963.1 ENSG00000251569.1 AC093899.2
chr2 169509701 169526262 36897 ENST00000284669.1 ENSG00000239474.6 KLHL41
•
written
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Luis Nassar
I do, currently QA at UCSC Genome Browser. Our main support address is genome@soe.ucsc.edu, but we keep an eye on biostars when we can (the UCSC tag helps).
Thanks for the comprehensive explanation Luis Nassar.
Let me give that a try and see if this solves by problem, and then I am going to accept this as an answer so that everyone could be benefited.
Hi Luis Nassar
How can I get a file from the knownGene table which look like this?
chrom transcript_start transcript_stop transcript_id gene symbol
chr1 11873 14409 uc010nxq.1 DDX11L1
chr1 14361 19759 uc009viu.3 WASH7P
chr1 14406 29370 uc009viw.2 WASH7P
chr1 34610 36081 uc001aak.3 FAM138F
chr1 69090 70008 uc001aal.1 OR4F5
chr1 134772 140566 uc021oeg.2 LOC729737
chr1 321083 321115 uc001aaq.2 DQ597235
chr1 321145 321207 uc001aar.2 DQ599768
chr1 322036 326938 uc009vjk.2 LOC100133331
Hello Vijay,
To get an output from the knownGene table like the one you described you will want to use the "selected fields from primary and related tables" option in the Table Browser:
Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables assembly: hg19 track: UCSC Genes table: knownGene output format: selected fields from primary and related tables get output Select Fields from hg19.knownGene: chrom, txStart, txEnd transcript select fields from hg19.kgXref fields: kgID, geneSymbol get output
Your output file should look like this (first 10 entries from chrom1):
#hg19.knownGene.chrom hg19.knownGene.txStart hg19.knownGene.txEnd hg19.kgXref.kgID hg19.kgXref.geneSymbol chr1 11873 14409 uc001aaa.3 DDX11L1 chr1 11873 14409 uc010nxr.1 DDX11L1 chr1 11873 14409 uc010nxq.1 DDX11L1 chr1 14361 16765 uc009vis.3 WASH7P chr1 14361 19759 uc009vit.3 WASH7P chr1 14361 19759 uc009viu.3 WASH7P chr1 14361 19759 uc001aae.4 WASH7P chr1 14361 29370 uc001aah.4 WASH7P chr1 14361 29370 uc009vir.3 WASH7P
If you would like to get this output with knownCanonical (like your example) you can follow the steps above with the following changes:
table: knownCanonical ... Select Fields from hg19.knownCanonical: chrom, chromStart, chromEnd transcript select fields from hg19.kgXref fields: kgID, geneSymbol
Your output file should look like this (first 10 entries from chrom1):
#hg19.knownCanonical.chrom hg19.knownCanonical.chromStart hg19.knownCanonical.chromEnd hg19.kgXref.kgID hg19.kgXref.geneSymbol chr1 11873 14409 uc010nxq.1 DDX11L1 chr1 14361 19759 uc009viu.3 WASH7P chr1 14406 29370 uc009viw.2 WASH7P chr1 34610 36081 uc001aak.3 FAM138F chr1 69090 70008 uc001aal.1 OR4F5 chr1 134772 140566 uc021oeg.2 LOC729737 chr1 321083 321115 uc001aaq.2 DQ597235 chr1 321145 321207 uc001aar.2 DQ599768 chr1 322036 326938 uc009vjk.2 LOC100133331 chr1 327545 328439 uc021oei.1 LOC388312
It may also be worth mentioning that our data tables (such as the example output) use 0-start, half open coordinates. If this is relevant you, we have a blog post on the topic: http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/
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UPDATE#1
In fact, I noticed that there are 1325 genes which are there in the
knownGenestable but not present inknownCanonicaltable.UPDATE#2
There is striking difference between the row counts of the 2 tables.
Schema for knownGene Row Count: 82,960
Schema for knownCanonical Row Count: 31,848
knownCanonicalis generally the longest isoform so it is not surprising that the number is smaller. See the definitions under Related Data section on this page.genomax I agree about the definition of "canonical". Numbers shown in the venn diagram are count of unique gene entries in both sets. Hence, it does not explain why the list of genes in "knownCanonical" is smaller (see Venn above). Every gene must have once canonical isoform.
Actually I am trying to replicate the steps mentioned in the below post:
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
The problem is that there are several genes missing from the final BED file.