View source for Gene Set Summary Statistics

==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==
<TABLE BORDER=1>
<TR><TH>db</TH><TH>gene<BR>count</TH><TH>total exon<BR>count</TH><TH>min exon<BR>count</TH><TH>max exon<BR>count</TH><TH>mean exon<BR>count</TH></TR>
<TR><TH>hg17</TH><TD ALIGN=RIGHT>39368</TD><TD ALIGN=RIGHT>405720</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>149</TD><TD ALIGN=RIGHT>10</TD></TR>
<TR><TH>hg18</TH><TD ALIGN=RIGHT>56722</TD><TD ALIGN=RIGHT>519308</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>2899</TD><TD ALIGN=RIGHT>9</TD></TR>
<TR><TH>mm8</TH><TD ALIGN=RIGHT>31863</TD><TD ALIGN=RIGHT>314628</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>313</TD><TD ALIGN=RIGHT>10</TD></TR>
<TR><TH>mm9</TH><TD ALIGN=RIGHT>49220</TD><TD ALIGN=RIGHT>417114</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>610</TD><TD ALIGN=RIGHT>8</TD></TR>
</TABLE>

==summary of exon size statistics==
<TABLE BORDER=1>
<TR><TH>db</TH><TH>sum exon<BR>sizes</TH><TH>min exon<BR>size</TH><TH>max exon<BR>size</TH><TH>mean exon<BR>size</TH></TR>
<TR><TH>hg17</TH><TD ALIGN=RIGHT>106839720</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>18172</TD><TD ALIGN=RIGHT>263</TD></TR>
<TR><TH>hg18</TH><TD ALIGN=RIGHT>146371091</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>36861</TD><TD ALIGN=RIGHT>282</TD></TR>
<TR><TH>mm8</TH><TD ALIGN=RIGHT>83159087</TD><TD ALIGN=RIGHT>4</TD><TD ALIGN=RIGHT>17497</TD><TD ALIGN=RIGHT>264</TD></TR>
<TR><TH>mm9</TH><TD ALIGN=RIGHT>117671086</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>29698</TD><TD ALIGN=RIGHT>282</TD></TR>
</TABLE>

==summary of intron size statistics==
<TABLE BORDER=1>
<TR><TH>db</TH><TH>sum intron<BR>sizes</TH><TH>min intron<BR>size</TH><TH>max intron<BR>size</TH><TH>mean intron<BR>size</TH></TR>
<TR><TH>hg17</TH><TD ALIGN=RIGHT>2223224397</TD><TD ALIGN=RIGHT>6</TD><TD ALIGN=RIGHT>1096450</TD><TD ALIGN=RIGHT>6069</TD></TR>
<TR><TH>hg18</TH><TD ALIGN=RIGHT>2784923600</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>1047320</TD><TD ALIGN=RIGHT>6023</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>
</TABLE>

==Top five exon count genes==
<TABLE BORDER=1>
<TR><TH>db</TH><TH COLSPAN=5>gene name (exon count)</TH></TR>
<TR><TH>hg17</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr2:152167363-152416454 NM_004543] (149)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr6:152534937-153050100 AF535142] (146)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr6:152534937-153050100 AF535142] (146)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr6:152534937-153050100 NM_033071] (146)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr6:152535029-153050648 AF495910] (146)</TD>
</TR>
<TR><TH>hg18</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr14:105065301-106352275 uc001yrq.1] (2899)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr22:20715572-21595078 uc002zvw.1] (322)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr2:179098964-179380395 uc002umr.1] (313)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr2:88937989-89411302 uc002stk.1] (217)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr2:179098964-179380395 uc002umt.1] (194)</TD>
</TR>
<TR><TH>mm8</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr2:76504823-76783386 NM_011652] (313)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr2:76504823-76783386 NM_028004] (192)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr9:108810682-108841812 NM_007738] (118)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr1:33956371-34252174 NM_134448] (99)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr4:122852023-123186663 DQ067088] (99)</TD>
</TR>
<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.cse.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.cse.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>
</TR>
</TABLE>

==Top five largest CDS extent genes==
<TABLE BORDER=1>
<TR><TH>db</TH><TH COLSPAN=5>gene name (CDS extent size: thickEnd-thickStart)</TH></TR>
<TR><TH>hg17</TH>
    <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:30897002-33117383 NM_000109] (2217347)</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:30897002-32989330 NM_004006] (2089394)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chrX:30898403-32989184 X14298] (2089394)</TD>
</TR>
<TR><TH>hg18</TH>
    <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:31047266-33267647 uc004ddb.1] (2217347)</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:31047266-33139594 uc004dda.1] (2089394)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr8:2782789-4839736 uc003wqd.1] (2055833)</TD>
</TR>
<TR><TH>mm8</TH>
    <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=chr6:44989695-47230955 NM_001004357] (2238304)</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=chr2:140086871-142081491 AK134694] (1988713)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr8:15895480-17535258 NM_053171] (1639258)</TD>
</TR>
<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.cse.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.cse.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>
</TR>
</TABLE>

==Top five smallest transcript genes==
<TABLE BORDER=1>
<TR><TH>db</TH><TH COLSPAN=5>gene name (transcript size:
txEnd-txStart)</TH></TR>
<TR><TH>hg17</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr4:69806230-69806397 AF241539] (168)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr7:129369319-129369494 AF277175] (176)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chrX:9353026-9353265 AY459291] (240)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr1:35869683-35869925 AY605064] (243)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr7:128643905-128644162 AF503918] (258)</TD>
</TR>
<TR><TH>hg18</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr9:130062323-130062342 uc004buj.1] (20)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:65874524-65874545 uc001dcm.1] (22)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr12:52671813-52671834 uc001seo.1] (22)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr12:56504708-56504729 uc001sqn.1] (22)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr20:15523127-15523148 uc002wpa.1] (22)</TD>
</TR>
<TR><TH>mm8</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chrX:12185020-12185236 AJ319753] (217)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr3:92585666-92585896 BC107019] (231)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr11:70546334-70546619 BC016221] (286)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr16:88757957-88758259 NM_130876] (303)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr16:88773645-88773948 NM_130873] (304)</TD>
</TR>
<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.cse.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.cse.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>
</TR>
</TABLE>

==Custom Track of Small Exons and Introns==


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

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==
[[Image:Hg17_hg18.exonCount.png]]
The caption on the graph above is incorrect.  The X axis is Exon Count per Gene

[[Image:Mm8_mm9.exonCount.png]]
The caption on the graph above is incorrect.  The X axis is Exon Count per Gene
<HR><HR><HR>

[[Image:Hg17_hg18.exonSize.png]]

[[Image:Mm8_mm9.exonSize.png]]

[[Image:Hg17_hg18_exonsTo300.png]]

[[Image:Mm8_mm9_exonsTo300.png]]

[[Image:Hg17_hg18.intronsTo170.png]]

[[Image:Mm8_mm9.intronsTo170.png]]

[[Image:Hg17_hg18.intronSize.png]]

[[Image:Mm8_mm9.intronSize.png]]

==Methods==

* From the table browser, request three different bed files for the knownGenes track:
# whole gene
# exons only
# introns only
* From those bed files, stats can be extracted
# gene count from: 'wc -l wholeGene.bed'
# exon count stats from:
<pre>
 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}'`
</pre>
* for exon or intron size stats:
<pre>
 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`
</pre>
* top five exon count genes
<pre>
sort -k10nr wholeGene.bed | head -5
</pre>
* top five CDS size genes
<pre>
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
</pre>
* top five smallest transcript genes
<pre>
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
</pre>