Gene Set Summary Statistics: Difference between revisions

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<TR><TH>db</TH><TH COLSPAN=5>gene name (CDS extent size: thickEnd-thickStart)</TH></TR>
<TR><TH>db</TH><TH COLSPAN=5>gene name (CDS extent size: thickEnd-thickStart)</TH></TR>
<TR><TH>hg17</TH>
<TR><TH>hg17</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr7:145251476-147555734 NM_014141] (2298740)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr7:145251477-147555734 NM_014141] (2298740)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chrX:30897001-33117383 NM_000109] (2217347)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chrX:30897002-33117383 NM_000109] (2217347)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr11:82846624-85015962 CR749820] (2138880)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr11:82846625-85015962 CR749820] (2138880)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chrX:30897001-32989330 NM_004006] (2089394)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chrX:30897002-32989330 NM_004006] (2089394)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chrX:30898402-32989184 X14298] (2089394)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chrX:30898403-32989184 X14298] (2089394)</TD>
</TR>
</TR>
<TR><TH>hg18</TH>
<TR><TH>hg18</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr7:145444385-147749019 uc003weu.1] (2298740)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr7:145444386-147749019 uc003weu.1] (2298740)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chrX:31047265-33267647 uc004ddb.1] (2217347)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chrX:31047266-33267647 uc004ddb.1] (2217347)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr11:82843700-85015962 uc001pak.1] (2138880)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr11:82843701-85015962 uc001pak.1] (2138880)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chrX:31047265-33139594 uc004dda.1] (2089394)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chrX:31047266-33139594 uc004dda.1] (2089394)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr8:2782788-4839736 uc003wqd.1] (2055833)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr8:2782789-4839736 uc003wqd.1] (2055833)</TD>
</TR>
</TR>
<TR><TH>mm8</TH>
<TR><TH>mm8</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chrX:79201621-81457760 NM_007868] (2253366)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chrX:79201622-81457760 NM_007868] (2253366)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr6:44989694-47230955 NM_001004357] (2238304)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr6:44989695-47230955 NM_001004357] (2238304)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr2:40418781-42475607 NM_053011] (2055883)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr2:40418782-42475607 NM_053011] (2055883)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr2:140086870-142081491 AK134694] (1988713)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr2:140086871-142081491 AK134694] (1988713)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr8:15895479-17535258 NM_053171] (1639258)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr8:15895480-17535258 NM_053171] (1639258)</TD>
</TR>
</TR>
<TR><TH>mm9</TH>
<TR><TH>mm9</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chrX:80194241-82450380 uc009tri.1] (2253366)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chrX:80194242-82450380 uc009tri.1] (2253366)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr6:45010086-47251368 uc009bst.1] (2238325)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr6:45010087-47251368 uc009bst.1] (2238325)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr16:39984483-42176405 uc007zfr.1] (2189582)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr16:39984484-42176405 uc007zfr.1] (2189582)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:40452292-42509118 uc008jon.1] (2055883)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:40452293-42509118 uc008jon.1] (2055883)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:140221165-142215786 uc008mpv.1] (1988713)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:140221166-142215786 uc008mpv.1] (1988713)</TD>
</TR>
</TR>
</TABLE>
</TABLE>

Revision as of 17:36, 19 September 2007

gene sets measured

  • hg17 - knownGenes version 2
  • hg18 - knownGenes version 3
  • mm8 - knownGenes version 2
  • mm9 - knownGenes version 3

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
mm831863314628131310
mm94922041711416108

summary of exon size statistics

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

summary of intron size statistics

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

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)
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)


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)
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)

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)
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)

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

Mm8 mm9.exonCount.png

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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