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Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics...
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Transcript of Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics...
![Page 1: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/1.jpg)
wfleabase.org/docs/tilexseq0904.pdf
What is all this genome expression?
Observations and statistics for expression at the base level
April 2009Don Gilbert Biology Dept., Indiana University
![Page 2: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/2.jpg)
wfleabase.org/docs/tilexseq0904.pdf
2007: Tile expression
DrosMel tiled by Affymetrix, finds new genes (blue) and known (orange)
.
![Page 3: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/3.jpg)
wfleabase.org/docs/tilexseq0904.pdf
Gene or Tiled expression?
Tiled genes find expression better than gene average
Gene median sensitivity 38%, specificity= 37% Tiled gene sensitivity= 42%, specificity= 37% in reference to separate sex expression study
![Page 4: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/4.jpg)
wfleabase.org/docs/tilexseq0904.pdf
Tiles find new genesDaphnia tile expression with gene finding calls 26% coding bases over the genome, compared to 17% from gene predictions, or 5,000 - 10,000 new genes.
Manak et al 2006, with Drosmel also found 24% CDS/genome, up from 18% CDS/genome from reference gene set. Computational tools need to mature; gene finding is preliminary.
QuickTime™ and a decompressor
are needed to see this picture.
![Page 5: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/5.jpg)
wfleabase.org/docs/tilexseq0904.pdf
Tiles find rarely used genes
New tile-genes are expressed in a subset of conditions, most known genes are expressed in all conditions
But some known genes have same low, spotty expression as Tile-genes
![Page 6: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/6.jpg)
wfleabase.org/docs/tilexseq0904.pdf
Tiles find rarely used genes
Average expression is high for genes found in all treatments
Accurate gene detection at low level expression remains a challenge
![Page 7: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/7.jpg)
wfleabase.org/docs/tilexseq0904.pdf
2008: Precision improves
Nimblegen has higher base precision than Affymetix
.
![Page 8: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/8.jpg)
wfleabase.org/docs/tilexseq0904.pdf
2009: Precision improves
RNA-Seq has higher base precision yet
And RNA-Seq here is strand-specific expression
Stranded
mRNA
ncRNA
![Page 9: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/9.jpg)
wfleabase.org/docs/tilexseq0904.pdf
Intron-Exon Detection
http://wfleabase.org/genome-summaries/tile-expression/tile-genestruct09/
![Page 10: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/10.jpg)
wfleabase.org/docs/tilexseq0904.pdf
Gene End Detection
http://wfleabase.org/genome-summaries/tile-expression/tile-genestruct09/
![Page 11: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/11.jpg)
wfleabase.org/docs/tilexseq0904.pdf
Differential expression
Gene end (3’) has more expression, but
constant differential over gene span, on average
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wfleabase.org/docs/tilexseq0904.pdf
Differential expression
Genes vary in DE pattern over gene span
i.e., a few parts may not capture full gene expression
![Page 13: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/13.jpg)
wfleabase.org/docs/tilexseq0904.pdf
Differential expression
Gene models miss much expression
Known sex genes capture DE, but unknown regions capture environmental stress expression, in Daphnia.
![Page 14: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/14.jpg)
wfleabase.org/docs/tilexseq0904.pdf
Differential eXp distribution
Introns show a null DE distribution, genes and TAR regions deviate from this. Use introns as baseline?
![Page 15: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/15.jpg)
wfleabase.org/docs/tilexseq0904.pdf
Stranded expression oddity
Expression in WRONG direction?
800 (3%) DrosMel Coding exons are expressed in wrong direction?
![Page 16: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/16.jpg)
wfleabase.org/docs/tilexseq0904.pdf
Stranded expression oddity
DrosMel transcript stranded expression (mRNA-Seq) picks up some odd cases.
Expression in BOTH directions?
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wfleabase.org/docs/tilexseq0904.pdf
Summary
1. Base-level expression (tiles, rna-seq) measures gene expression better
• Balances sensitivity (false rejection) with specificity (false discovery)
2. Genome-wide base-level expression finds new genes• As an alternative to gene-level studies, it has values and drawbacks.
Computational methods need to improve to use this data well.
3. Base-level expression measures gene structures well• On average, and precision is improving for individual genes.• Gene oddities are found also
![Page 18: Wfleabase.org/docs/tilexseq0904.pdf What is all this genome expression? Observations and statistics for expression at the base level April 2009Don Gilbert.](https://reader036.fdocuments.us/reader036/viewer/2022081603/56649efd5503460f94c1192a/html5/thumbnails/18.jpg)
wfleabase.org/docs/tilexseq0904.pdf
End note
Summary pageswfleabase.org/genome-summaries/tile-expression/
insects.eugenes.org/species/data/dmel5/modencode/
Genome expression mapsinsects.eugenes.org:8091/gbrowse/cgi-bin/gbrowse/drosmelme/
• expression in 52 cell lines (affy) and more precise solexa & nimblegen for a few cell lines
insects.eugenes.org:8091/gbrowse/cgi-bin/gbrowse/daphnia_pulex8/• expression among 4 treatment groups (sex, metal stress, biotic predator);
nimblegen