Gene Set Summary Statistics: Difference between revisions
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==Histogram graphs== | ==Histogram graphs== | ||
[[Image:hg17-hg18.exonCount.png]] | [[Image:hg17-hg18.exonCount.png]] | ||
[[Image:Mm8_mm9_exonsTo300.png]] | |||
==Methods== | ==Methods== | ||
Revision as of 16:34, 18 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) |
Histogram graphs
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:
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
