my seminar in 6/15

1. Assessing Computational Methods for
Transcription Factor Target Gene Identification
Based on ChIP-seq Data
Advisor: Dr. Chun-Chi Liu
Speaker: Yu-Jung Chiu
Date: 2015/6/15
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2. Outline
• Introduction
• Materials and Methods
• Results
• Discussion
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3. Introduction
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4. ChIP-Seq
4Mardis E, Nature Methods (2007)
Peter J. Park, Nature Reviews (2009)
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5. Peak
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Reference genome
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Peter V Kharchenko, Nature(2008)

6. Binding Profile
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Chao Cheng, NAR(2011)

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Materials and Methods

8. ChIP-seq data
• HemoChIP (hematopoietic cells)：
30 transcription factors
• ESChIP (embryonic stem cells)：
15 transcription factors
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9. Expression data
• HemoChIP ： 30 expression data
• ESChIP ： 15 expression data
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10. scoring procedure
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11. TF-target prediction methods
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Results

13. Perturbation expression data
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14. Differential TF activity data
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15. Functional homogeneity of targets
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16. Consistency and specificity of target predictions
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17. Gene density around predicted targets
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Discussion

19. Discussion
• Out of six compared methods, Binary and Chen clearly
performed the worst.
• other methods performed similarly, but we observed a
small advantage of ClosestGene especially in the
expression data tests and GO enrichment.
• all of our analysis is based on mouse data , similar
assessments should be performed for other species.
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Thank You

21. Supplementary
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