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Update on Adjacent Gene Analysis - Meeting Summary

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koen
18 diapositives · 268 Views · Sep 18, 2014

Summary of a meeting held on February 26, 2009 by Mark Borodovsky and Ivan Antonov at GATech discussing recent results and future work on analyzing adjacent genes. Topics covered include bug fixes, threshold adjustments for gap length and RBS site scores, genes distribution, reducing false negatives and positives, and FSMark-GM predictions.

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  1. Regular MeetingFebruary 26, 2009 Mark Borodovsky Ivan Antonov

  2. Topics • What have been done • Results for adjacent genes using bigger gap length • Results for adjacent genes using RBS site threshold • Future work GATech

  3. What have been done • A small bug in calculating gene statistics found • Bigger threshold on gap length in adjacent genes is used • RBS site score threshold is implemented GATech

  4. Bug-free statistics

  5. Typical genes distribution (old) 400 typical genes with FS Green squares – where “All others” principle was used End/start missing End missing Start missing End/start present 1 27 15 357 Gap len >60 53 Adjacent genes Gene overlap 114 167 190 Gap len <60 GATech

  6. Typical genes distribution (new) 400 typical genes with FS Green squares – where “All others” principle was used End/start missing End missing Start missing End/start present 1 34 26 339 Gap len >60 35 Adjacent genes Gene overlap 114 149 190 Gap len <60 GATech

  7. Reducing number ofFalse Negatives among adjacent genesby increasing upper bound threshold on gap length

  8. Choosing upper bound threshold Old Threshold 60 New Threshold 160 29 FS adjacent genes more GATech

  9. FS genes distribution 400 typical genes with FS Green squares – where “All others” principle was used End/start missing End missing Start missing End/start present 1 34 26 339 Gap len >160 6 Adjacent genes Gene overlap 143 149 190 Gap len <160 GATech

  10. FSMark-GM prediction GeneMark Output Numbers of FS genes are in brackets Adjacent Genes Gene Overlaps 1238 (143) 366 (190) FSMark applied 256 (145) 418 (103) GATech

  11. Reducing number ofFalse Positives among adjacent genesby introducing threshold on maximum value of RBS site score

  12. Downstream gene RBS site score distribution GATech

  13. Downstream gene RBS site score distribution GATech

  14. FS genes distribution 400 typical genes with FS Green squares – where “All others” principle was used End/start missing End missing Start missing End/start present 1 34 26 339 Gap len >160 23 Adjacent genes Gene overlap 126 149 190 Gap len <160 GATech

  15. FSMark-GM prediction GeneMark Output Gene Overlaps Adjacent Genes TP FP 176 190 501 126 FSMark applied 111 145 131 92 GATech

  16. Today’s FSMark-GM performance GATech

  17. Conclusions • Bigger gap threshold slightly increased number of True Positives in adjacent genes • RBS site score threshold significantly decreased number of False positives in adjacent genes GATech

  18. Future work • Try to understand why do we have so many genes with end missing • Take closer look at FSMark results on adjacent genes • What else? GATech