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Comparative Analysis of RNA Expression Levels Reveals Gene Differences in MAQ and Exonerate Submissions

This study compares RPKM expression levels from Gun, Mar, Tyl, and Vic groups to identify genes with significant differences in submitted models. Results show varying levels of difference across loci, with distinct patterns in gene expression.

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Comparative Analysis of RNA Expression Levels Reveals Gene Differences in MAQ and Exonerate Submissions

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  1. RGASP Gary Williams

  2. Exonerate vs cufflinks

  3. Cufflinks vs MAQ

  4. Exonerate vs MAQ

  5. Comparing submitted models • Have submissions from groups: Gun, Mar, Tyl, Vic • Want to look at models that are different. • Fast way to find these is to look at RPKM expression levels.

  6. Typical expression levels RPKM of locus

  7. Want loci which differ • Took maximum RPKM of loci from each group. • Compare the RPKM levels to find genes where there is a big difference in one or more submissions. • Gun & Vic submissions have no mitochondrial genes, assume these were not looked at. • 4% of 20,000 loci no difference, 9% less than 50% difference, 76% have >50% difference, 13% have 100% difference (zero & not zero values).

  8. B0513.3 • Gun: 14,468 Mar: 4,337 Tyl: 1,145 Vic: 4,636 • Well formed, highly expressed, no problem

  9. B0412.4 • Gun: 9,629 Mar: 3,980 Tyl: 31 Vic: 3,738 • Well formed, highly expressed, snoRNAs in introns

  10. M01H9.1 • Gun: 33 Mar: 1 Tyl: 4 Vic: 24 • Well formed, medium expression, new isoform extending exon 3?

  11. F26F2.2 • Gun: 0.5 Mar: 0.1 Tyl: 0.03 Vic: 0.95 • Well formed, low expression, exons 1&2 not unique in genome, isoform starting at exon 3

  12. C05G5.7 • Gun: 155 Mar: 0 Tyl: 0 Vic: 121 • Well formed single exon, high expression.

  13. Y105C5A.12 • Gun: 182 Mar: 0 Tyl: 58 Vic: 223 • Copy of part of nearby gene, high expression.

  14. END

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