O slideshow foi denunciado.
A knowledge-based strategy for structural recognition of transcription factor binding sites Beisi Xu Laboratory of Molecul...
Central Dogma http://stemcells.nih.gov
Central Dogma
Eukaryotic Model
Transcription wiki
Before Transcription
Yeast TFBS Database <ul><li>TRANSFAC </li></ul><ul><ul><li>Commercial  </li></ul></ul><ul><ul><li>Experimental </li></ul><...
TFBS <ul><li>Conserved Sequence </li></ul><ul><ul><li>Most probability base </li></ul></ul><ul><ul><li>Lost information </...
TFBS Prediction Methods <ul><li>de novo </li></ul><ul><ul><li>MEME,AlignACE,BioProspector </li></ul></ul><ul><ul><li>Motif...
Reference State
Volume-Correction & Dirichlet pseudocounts for low-counts
Optimization I
Optimization II
Optimization III
Optimization III
Correction Combination Result
Transcription Factor Binding Sites(TFBS )
Prediction Process
Threading Energy
Match Experiment Result
DNA strucuture rotation and translation
Compare of training set
Prediction Accuracy
Comparing to Other Methods
ROC curves for MCM1
Energy Grid Map
Lower Energy Grid Map
Forbidden Block of Protein
Native Structure
 
A-DNA,B-DNA,Z-DNA
 
Próximos SlideShares
Carregando em…5
×

A knowledge-based strategy for structural recognition of transcription factor binding sites

1.383 visualizações

Publicada em

A knowledge-based strategy for structural recognition of transcription factor binding sites

Publicada em: Educação
  • Seja o primeiro a comentar

A knowledge-based strategy for structural recognition of transcription factor binding sites

  1. 1. A knowledge-based strategy for structural recognition of transcription factor binding sites Beisi Xu Laboratory of Molecular Modeling and Design Dalian Institute of Chemical Physical xubeisi [at] gmail.com
  2. 2. Central Dogma http://stemcells.nih.gov
  3. 3. Central Dogma
  4. 4. Eukaryotic Model
  5. 5. Transcription wiki
  6. 6. Before Transcription
  7. 7. Yeast TFBS Database <ul><li>TRANSFAC </li></ul><ul><ul><li>Commercial </li></ul></ul><ul><ul><li>Experimental </li></ul></ul><ul><ul><li>Redundancy </li></ul></ul><ul><li>JASPAR </li></ul><ul><ul><li>Open </li></ul></ul><ul><ul><li>Only PWM </li></ul></ul><ul><ul><li>Non redundancy </li></ul></ul><ul><li>SELEX_DB & HTPSELEX </li></ul><ul><ul><li>SELEX experiment </li></ul></ul><ul><li>SCPD,MYBS </li></ul>
  8. 8. TFBS <ul><li>Conserved Sequence </li></ul><ul><ul><li>Most probability base </li></ul></ul><ul><ul><li>Lost information </li></ul></ul><ul><li>Position Weight Matrix(PWM) </li></ul>jaspar <ul><ul><li>Example: </li></ul></ul><ul><ul><li>AAAA </li></ul></ul><ul><ul><li>ACCA </li></ul></ul><ul><ul><li>ACTG AAAA </li></ul></ul><ul><ul><li>CAAC </li></ul></ul><ul><ul><li>CAGT </li></ul></ul>
  9. 9. TFBS Prediction Methods <ul><li>de novo </li></ul><ul><ul><li>MEME,AlignACE,BioProspector </li></ul></ul><ul><ul><li>MotifVoter 275% better </li></ul></ul><ul><ul><li>CisModule 56% </li></ul></ul><ul><li>Chip-array data </li></ul><ul><ul><li>Mdscan,MatrixREDUCE,RankMotif++ </li></ul></ul><ul><ul><li>MeDiChI chip-tiling </li></ul></ul><ul><ul><li>QuEST,MICSA chip-seq </li></ul></ul><ul><li>Phylogenetic Footprinting </li></ul><ul><ul><li>CompareProspector </li></ul></ul><ul><ul><li>PhyloGibbs </li></ul></ul><ul><ul><li>PhyME </li></ul></ul>
  10. 10. Reference State
  11. 11. Volume-Correction & Dirichlet pseudocounts for low-counts
  12. 12. Optimization I
  13. 13. Optimization II
  14. 14. Optimization III
  15. 15. Optimization III
  16. 16. Correction Combination Result
  17. 17. Transcription Factor Binding Sites(TFBS )
  18. 18. Prediction Process
  19. 19. Threading Energy
  20. 20. Match Experiment Result
  21. 21. DNA strucuture rotation and translation
  22. 22. Compare of training set
  23. 23. Prediction Accuracy
  24. 24. Comparing to Other Methods
  25. 25. ROC curves for MCM1
  26. 26. Energy Grid Map
  27. 27. Lower Energy Grid Map
  28. 28. Forbidden Block of Protein
  29. 29. Native Structure
  30. 31. A-DNA,B-DNA,Z-DNA

×