Gene Set Summary Statistics: Difference between revisions

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(Updated genome-test or hgwdev links from .cse/.soe to .gi, most links validated)
 
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* hg17 - knownGenes version 2
* hg17 - knownGenes version 2
* hg18 - knownGenes version 3
* hg18 - knownGenes version 3
* hg19 - knownGenes version 7
* mm8 - knownGenes version 2
* mm8 - knownGenes version 2
* mm9 - knownGenes version 3
* mm9 - knownGenes version 3
* mm10 - knownGenes version 6


The min, max and mean measurements are ''per gene''
The min, max and mean measurements are ''per gene''
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<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>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>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>hg19</TH><TD ALIGN=RIGHT>82960</TD><TD ALIGN=RIGHT>742493</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>5065</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>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>
<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>
<TR><TH>mm10</TH><TD ALIGN=RIGHT>59121</TD><TD ALIGN=RIGHT>486425</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>813</TD><TD ALIGN=RIGHT>8</TD></TR>
</TABLE>
</TABLE>


Line 21: Line 25:
<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>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>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>hg19</TH><TD ALIGN=RIGHT>221924089</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>205012</TD><TD ALIGN=RIGHT>299</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>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>
<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>
<TR><TH>mm10</TH><TD ALIGN=RIGHT>143087341</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>83437</TD><TD ALIGN=RIGHT>294</TD></TR>
</TABLE>
</TABLE>


Line 30: Line 36:
<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>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>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>hg19</TH><TD ALIGN=RIGHT>4127555916</TD><TD ALIGN=RIGHT>1</TD><TD ALIGN=RIGHT>1160410</TD><TD ALIGN=RIGHT>6260</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>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>


Line 38: Line 46:
<TR><TH>db</TH><TH COLSPAN=5>gene name (exon count)</TH></TR>
<TR><TH>db</TH><TH COLSPAN=5>gene name (exon count)</TH></TR>
<TR><TH>hg17</TH>
<TR><TH>hg17</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr2:152167362-152416454 NM_004543] (149)</TD>
     <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=chr6:152534936-153050100 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=chr6:152534936-153050100 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=chr6:152534936-153050100 NM_033071] (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=chr6:152535028-153050648 AF495910] (146)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr6:152535029-153050648 AF495910] (146)</TD>
</TR>
</TR>
<TR><TH>hg18</TH>
<TR><TH>hg18</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr14:105065300-106352275 uc001yrq.1] (2899)</TD>
     <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=chr22:20715571-21595078 uc002zvw.1] (322)</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=chr2:179098963-179380395 uc002umr.1] (313)</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=chr2:88937988-89411302 uc002stk.1] (217)</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=chr2:179098963-179380395 uc002umt.1] (194)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr2:179098964-179380395 uc002umt.1] (194)</TD>
</TR>
<TR><TH>hg19</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr14:105994256-107283085 uc031qqx.1] (5065)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr22:22385572-23265082 uc031rxg.1] (462)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr2:179390717-179672150 uc031rqc.1] (363)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr2:179390717-179672150 uc031rqd.1] (313)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr2:179390717-179672150 uc021vsy.2] (312)</TD>
</TR>
</TR>
<TR><TH>mm8</TH>
<TR><TH>mm8</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr2:76504822-76783386 NM_011652] (313)</TD>
     <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=chr2:76504822-76783386 NM_028004] (192)</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=chr9:108810681-108841812 NM_007738] (118)</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=chr1:33956370-34252174 NM_134448] (99)</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=chr4:122852022-123186663 DQ067088] (99)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr4:122852023-123186663 DQ067088] (99)</TD>
</TR>
</TR>
<TR><TH>mm9</TH>
<TR><TH>mm9</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr12:114498399-117248164 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.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:76542040-76820604 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.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:76542040-76820604 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.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr2:51992166-52194318 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.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr9:108855789-108886920 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>


==Top five largest CDS extent genes==
==Top five largest CDS extent genes==
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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><TH>hg19</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:144146811-146467744 uc021ott.2] (2307732)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr7:145813453-148118088 uc003weu.2] (2298740)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chrX:31137345-33357726 uc004ddb.1] (2217347)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr11:83166056-85338314 uc001pak.2] (2138880)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chrX:31137345-33229673 uc004dda.1] (2089394)</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-test.gi.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-test.gi.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-test.gi.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-test.gi.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-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>


Line 106: Line 139:
txEnd-txStart)</TH></TR>
txEnd-txStart)</TH></TR>
<TR><TH>hg17</TH>
<TR><TH>hg17</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr4:69806229-69806397 AF241539] (168)</TD>
     <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=chr7:129369318-129369494 AF277175] (176)</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:9353025-9353265 AY459291] (240)</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=chr1:35869682-35869925 AY605064] (243)</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=chr7:128643904-128644162 AF503918] (258)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr7:128643905-128644162 AF503918] (258)</TD>
</TR>
</TR>
<TR><TH>hg18</TH>
<TR><TH>hg18</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr9:130062322-130062342 uc004buj.1] (20)</TD>
     <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=chr1:65874523-65874545 uc001dcm.1] (22)</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=chr12:52671812-52671834 uc001seo.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=chr12:56504707-56504729 uc001sqn.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=chr20:15523126-15523148 uc002wpa.1] (22)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr20:15523127-15523148 uc002wpa.1] (22)</TD>
</TR>
<TR><TH>hg19</TH>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr10:122806840-122806858 uc031pxj.1] (19)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr12:58034966-58034984 uc021qzo.1] (19)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:179170963-179170982 uc021pfi.1] (20)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:68649302-68649321 uc021oot.1] (20)</TD>
    <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr10:134958378-134958397 uc021qbd.1] (20)</TD>
</TR>
</TR>
<TR><TH>mm8</TH>
<TR><TH>mm8</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chrX:12185019-12185236 AJ319753] (217)</TD>
     <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=chr3:92585665-92585896 BC107019] (231)</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=chr11:70546333-70546619 BC016221] (286)</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=chr16:88757956-88758259 NM_130876] (303)</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=chr16:88773644-88773948 NM_130873] (304)</TD>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr16:88773645-88773948 NM_130873] (304)</TD>
</TR>
</TR>
<TR><TH>mm9</TH>
<TR><TH>mm9</TH>
     <TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr1:74440897-74440919 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.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr10:85230423-85230445 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.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr11:77886548-77886570 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.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr12:110831097-110831119 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.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr13:54944552-54944574 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>


==Custom Track of Small Exons and Introns==
Custom 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 small exons and introns are used to maintain frame coding boundaries
as found in mRNAs compared to the reference genome coordinates.


==Histogram graphs==
==Histogram graphs==
[[Image:hg17-hg18.exonCount.png]]
[[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: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==
==Methods==
Line 183: Line 258:
}' wholeGene.bed | sort -k5n | head -5
}' wholeGene.bed | sort -k5n | head -5
</pre>
</pre>
[[Category:Gene Set Summary Statistics]]

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