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

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
hg19	82960	742493	1	5065	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
hg19	221924089	1	205012	299
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)

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

The caption on the graph above is incorrect. The X axis is Exon Count per Gene

The caption on the graph above is incorrect. The X axis is Exon Count per Gene

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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