Gene Set Summary Statistics: Difference between revisions

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<TR><TH>mm8</TH><TD ALIGN=RIGHT>1476081990</TD><TD ALIGN=RIGHT>9</TD><TD ALIGN=RIGHT>1347550</TD><TD ALIGN=RIGHT>5220</TD></TR>
<TR><TH>mm8</TH><TD ALIGN=RIGHT>1476081990</TD><TD ALIGN=RIGHT>9</TD><TD ALIGN=RIGHT>1347550</TD><TD ALIGN=RIGHT>5220</TD></TR>
<TR><TH>mm9</TH><TD ALIGN=RIGHT>2055504784</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>1253430</TD><TD ALIGN=RIGHT>5589</TD></TR>
<TR><TH>mm9</TH><TD ALIGN=RIGHT>2055504784</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>1253430</TD><TD ALIGN=RIGHT>5589</TD></TR>
<TR><TH>mm10</TH><TD ALIGN=RIGHT>2420504661</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>3003780</TD><TD ALIGN=RIGHT>5665</TD></TR>
</TABLE>
</TABLE>


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</TR>
</TR>
<TR><TH>mm9</TH>
<TR><TH>mm9</TH>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr12:114498400-117248164 uc007pgj.1] (610)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr12:114498400-117248164 uc007pgj.1] (610)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:76542041-76820604 uc008kfn.1] (313)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:76542041-76820604 uc008kfn.1] (313)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:76542041-76820604 uc008kfo.1] (192)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:76542041-76820604 uc008kfo.1] (192)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:51992167-52194318 uc008jqv.1] (157)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:51992167-52194318 uc008jqv.1] (157)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr9:108855790-108886920 uc009rrh.1] (118)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr9:108855790-108886920 uc009rrh.1] (118)</TD>
</TR>
</TR>
<TR><TH>mm10</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr12:113260189-116009879 uc029ryi.1] (813)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr2:76703984-76982547 uc008kfn.1] (313)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr2:76703984-76982547 uc008kfo.1] (192)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr2:52136647-52338798 uc008jqv.1] (157)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr9:108953745-108984875 uc009rrh.1] (118)</TD>
</TABLE>
</TABLE>


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</TR>
</TR>
<TR><TH>mm9</TH>
<TR><TH>mm9</TH>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chrX:80194242-82450380 uc009tri.1] (2253366)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chrX:80194242-82450380 uc009tri.1] (2253366)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr6:45010087-47251368 uc009bst.1] (2238325)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr6:45010087-47251368 uc009bst.1] (2238325)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr16:39984484-42176405 uc007zfr.1] (2189582)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr16:39984484-42176405 uc007zfr.1] (2189582)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:40452293-42509118 uc008jon.1] (2055883)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:40452293-42509118 uc008jon.1] (2055883)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:140221166-142215786 uc008mpv.1] (1988713)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:140221166-142215786 uc008mpv.1] (1988713)</TD>
</TR>
</TR>
<TR><TH>mm10</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chrX:82948870-85205050 uc009tri.2] (2253366)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr6:45060061-47301371 uc009bst.2] (2238325)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr16:39984371-42176292 uc007zfr.1](2189582)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr2:40596773-42653598 uc008jon.1] (2055883)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr2:140395430-142390050 uc008mpv.1] (1988713)</TD>
</TABLE>
</TABLE>


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</TR>
</TR>
<TR><TH>mm9</TH>
<TR><TH>mm9</TH>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr1:74440898-74440919 uc007bma.1] (22)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr1:74440898-74440919 uc007bma.1] (22)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr10:85230424-85230445 uc007gmr.1] (22)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr10:85230424-85230445 uc007gmr.1] (22)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr11:77886549-77886570 uc007khz.1] (22)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr11:77886549-77886570 uc007khz.1] (22)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr12:110831098-110831119 uc007pay.1] (22)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr12:110831098-110831119 uc007pay.1] (22)</TD>
     <TD>[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr13:54944553-54944574 uc007qpn.1] (22)</TD>
     <TD>[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr13:54944553-54944574 uc007qpn.1] (22)</TD>
</TR>
<TR><TH>mm10</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr17:15192492-15192509 uc029tak.1] (18)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr1:137031387-137031406 uc029qtn.1] (20)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr1:187624235-187624254 uc029qvd.1] (20)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr1:82585127-82585146 uc029qpl.1] (20)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr11:46266296-46266315 uc029rlk.1] (20)</TD>
</TR>
</TR>
</TABLE>
</TABLE>
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Custom track:  
Custom track:  
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/3/37/Hg18KnownGenesSmallIntronsExonsCt.txt.gz Hg18 small exons and introns] on the UCSC Genes track
[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genomewiki.ucsc.edu/images/3/37/Hg18KnownGenesSmallIntronsExonsCt.txt.gz Hg18 small exons and introns] on the UCSC Genes track


These are exons of size less than 22 bases, and introns of size less than 12 bases.  The score column contains the size and thus you can filter smaller subsets via the score column in the table browser.
These are exons of size less than 22 bases, and introns of size less than 12 bases.  The score column contains the size and thus you can filter smaller subsets via the score column in the table browser.

Latest revision as of 22:01, 31 August 2018

gene sets measured

  • hg17 - knownGenes version 2
  • hg18 - knownGenes version 3
  • hg19 - knownGenes version 7
  • mm8 - knownGenes version 2
  • mm9 - knownGenes version 3
  • mm10 - knownGenes version 6

The min, max and mean measurements are per gene

summary of gene and exon counts

dbgene
count		total exon
count		min exon
count		max exon
count		mean exon
count
hg1739368405720114910
hg1856722519308128999
hg1982960742493150659
mm831863314628131310
mm94922041711416108
mm105912148642518138

summary of exon size statistics

dbsum exon
sizes		min exon
size		max exon
size		mean exon
size
hg17106839720118172263
hg18146371091136861282
hg192219240891205012299
mm883159087417497264
mm9117671086129698282
mm10143087341183437294

summary of intron size statistics

dbsum intron
sizes		min intron
size		max intron
size		mean intron
size
hg172223224397610964506069
hg182784923600110473206023
hg194127555916111604106260
mm81476081990913475505220
mm92055504784112534305589
mm102420504661130037805665

Top five exon count genes

dbgene name (exon count)
hg17 NM_004543 (149) AF535142 (146) AF535142 (146) NM_033071 (146) AF495910 (146)
hg18 uc001yrq.1 (2899) uc002zvw.1 (322) uc002umr.1 (313) uc002stk.1 (217) uc002umt.1 (194)
hg19 uc031qqx.1 (5065) uc031rxg.1 (462) uc031rqc.1 (363) uc031rqd.1 (313) uc021vsy.2 (312)
mm8 NM_011652 (313) NM_028004 (192) NM_007738 (118) NM_134448 (99) DQ067088 (99)
mm9 uc007pgj.1 (610) uc008kfn.1 (313) uc008kfo.1 (192) uc008jqv.1 (157) uc009rrh.1 (118)
mm10 uc029ryi.1 (813) uc008kfn.1 (313) uc008kfo.1 (192) uc008jqv.1 (157) uc009rrh.1 (118)

Top five largest CDS extent genes

dbgene name (CDS extent size: thickEnd-thickStart)
hg17 NM_014141 (2298740) NM_000109 (2217347) CR749820 (2138880) NM_004006 (2089394) X14298 (2089394)
hg18 uc003weu.1 (2298740) uc004ddb.1 (2217347) uc001pak.1 (2138880) uc004dda.1 (2089394) uc003wqd.1 (2055833)
hg19 uc021ott.2 (2307732) uc003weu.2 (2298740) uc004ddb.1 (2217347) uc001pak.2 (2138880) uc004dda.1 (2089394)
mm8 NM_007868 (2253366) NM_001004357 (2238304) NM_053011 (2055883) AK134694 (1988713) NM_053171 (1639258)
mm9 uc009tri.1 (2253366) uc009bst.1 (2238325) uc007zfr.1 (2189582) uc008jon.1 (2055883) uc008mpv.1 (1988713)
mm10 uc009tri.2 (2253366) uc009bst.2 (2238325) uc007zfr.1(2189582) uc008jon.1 (2055883) uc008mpv.1 (1988713)

Top five smallest transcript genes

dbgene name (transcript size: txEnd-txStart)
hg17 AF241539 (168) AF277175 (176) AY459291 (240) AY605064 (243) AF503918 (258)
hg18 uc004buj.1 (20) uc001dcm.1 (22) uc001seo.1 (22) uc001sqn.1 (22) uc002wpa.1 (22)
hg19 uc031pxj.1 (19) uc021qzo.1 (19) uc021pfi.1 (20) uc021oot.1 (20) uc021qbd.1 (20)
mm8 AJ319753 (217) BC107019 (231) BC016221 (286) NM_130876 (303) NM_130873 (304)
mm9 uc007bma.1 (22) uc007gmr.1 (22) uc007khz.1 (22) uc007pay.1 (22) uc007qpn.1 (22)
mm10 uc029tak.1 (18) uc029qtn.1 (20) uc029qvd.1 (20) uc029qpl.1 (20) uc029rlk.1 (20)

Custom Track of Small Exons and Introns

Custom track: Hg18 small exons and introns on the UCSC Genes track

These are exons of size less than 22 bases, and introns of size less than 12 bases. The score column contains the size and thus you can filter smaller subsets via the score column in the table browser.

These small exons and introns are used to maintain frame coding boundaries as found in mRNAs compared to the reference genome coordinates.

Histogram graphs

Hg17 hg18.exonCount.png The caption on the graph above is incorrect. The X axis is Exon Count per Gene

Mm8 mm9.exonCount.png The caption on the graph above is incorrect. The X axis is Exon Count per Gene

Hg17 hg18.exonSize.png

Mm8 mm9.exonSize.png

Hg17 hg18 exonsTo300.png

Mm8 mm9 exonsTo300.png

Hg17 hg18.intronsTo170.png

Mm8 mm9.intronsTo170.png

Hg17 hg18.intronSize.png

Mm8 mm9.intronSize.png

Methods

  • From the table browser, request three different bed files for the knownGenes track:
  1. whole gene
  2. exons only
  3. introns only
  • From those bed files, stats can be extracted
  1. gene count from: 'wc -l wholeGene.bed'
  2. exon count stats from:
 STATS=`ave -col=10 wholeGene.bed -tableOut | grep -v "^#"`
 MIN=`echo $STATS | cut -d' ' -f1`
 MAX=`echo $STATS | cut -d' ' -f5`
 MEAN=`echo $STATS | cut -d' ' -f6 | awk '{printf "%d", $1+0.5}'`
 COUNT=`echo $STATS | cut -d' ' -f8 | awk '{printf "%d", $1}'`
  • for exon or intron size stats:
 STATS=`awk '{print $3-$2}' {introns,exons}.bed \
      | ave -col=1 stdin -tableOut | grep -v "^#"`
 MIN=`echo $STATS | cut -d' ' -f1`
 MAX=`echo $STATS | cut -d' ' -f5 | awk '{printf "%d", $1}'`
 MEAN=`echo $STATS | cut -d' ' -f6 | awk '{printf "%d", $1+0.5}'`
 SUM_SIZE=`awk '{sum += $3-$2} END{printf "%d", sum}' {introns,exons}.bed`
  • top five exon count genes
sort -k10nr wholeGene.bed | head -5
  • top five CDS size genes
awk '{cdsSize=$8-$7
if (cdsSize > 0) {printf "%s\t%s\t%s\t%s\t%d\n", $1,$2,$3,$4,cdsSize}
}' wholeGene.bed | sort -k5nr | head -5
  • top five smallest transcript genes
awk '{size=$3-$2
if (size > 0) {printf "%s\t%s\t%s\t%s\t%d\n", $1,$2,$3,$4,size}
}' wholeGene.bed | sort -k5n | head -5
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