Gene Set Summary Statistics: Difference between revisions
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<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=chr2:40452292-42509118 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=chr2:140221165-142215786 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=chr4:69806229-69806397 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=chrX:9353025-9353265 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=chr7:128643904-128644162 AF503918] (258)</TD> | |||
</TR> | |||
<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=chr1:65874523-65874545 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=chr12:56504707-56504729 uc001sqn.1] (22)</TD> | |||
<TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr20:15523126-15523148 uc002wpa.1] (22)</TD> | |||
</TR> | |||
<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=chr3:92585665-92585896 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=chr16:88757956-88758259 NM_130876] (303)</TD> | |||
<TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&position=chr16:88773644-88773948 NM_130873] (304)</TD> | |||
</TR> | |||
<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.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr10:85230423-85230445 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.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr12:110831097-110831119 uc007pay.1] (22)</TD> | |||
<TD>[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr13:54944552-54944574 uc007qpn.1] (22)</TD> | |||
</TR> | </TR> | ||
</TABLE> | </TABLE> | ||
Revision as of 22:36, 14 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
| db | gene count | total exon count | min exon count | max exon count | mean exon count |
|---|---|---|---|---|---|
| hg17 | 39368 | 405720 | 1 | 149 | 10 |
| hg18 | 56722 | 519308 | 1 | 2899 | 9 |
| mm8 | 31863 | 314628 | 1 | 313 | 10 |
| mm9 | 49220 | 417114 | 1 | 610 | 8 |
summary of exon size statistics
| db | sum exon sizes | min exon size | max exon size | mean exon size |
|---|---|---|---|---|
| hg17 | 106839720 | 1 | 18172 | 263 |
| hg18 | 146371091 | 1 | 36861 | 282 |
| mm8 | 83159087 | 4 | 17497 | 264 |
| mm9 | 117671086 | 1 | 29698 | 282 |
summary of intron size statistics
| db | sum intron sizes | min intron size | max intron size | mean intron size |
|---|---|---|---|---|
| hg17 | 2223224397 | 6 | 1096450 | 6069 |
| hg18 | 2784923600 | 1 | 1047320 | 6023 |
| mm8 | 1476081990 | 9 | 1347550 | 5220 |
| mm9 | 2055504784 | 1 | 1253430 | 5589 |
Top five exon count genes
| db | gene 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
| db | gene 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
| db | gene 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) |
