Satellite meeting for Transcription regulation

Topics

Biologists need to get more detailed information about what is happening a gene level when they look at microarray data:

• Enrichment analysis of TFBS ()
• Transcription factor binding site SNPs ()
• Histone binding
• Network analysis (which genes are interesting??)
• Expression levels
• siRNA, miRNA that control function
• Methylation
• Copy number variation
• Protein structure of TFs

Attendees

• Riu Yamashita
• Young Joo Kim
• Alberto Labarga

Date

• 2009/3/17 11:00-12:00

Room

• Chura hall (3F)

Notes

Results

TODOs

Transcriptional regulation Genomic variation(SNP, CNV….) using NGS Data, sequence Variation detection, Annotation

Dr. Liu ,

Purpose: Make a unified solution tool that biologists want in their functional, molecular studies. -Identify feasible techniques and economic solutions for them.

The questions that should be addressed. 1. Transcription binding sites, modulations 2. Histon binding sites 3. Histon modification 4. SNPs, SNP chips 5. Expression (mRNA or cDNA chips) 6. miRNA or RNAi 7. methylation (epigenetics) 8. CNV (copy number variation) 9. Protein structure 10. Protein chips 11. Tissue arrays 12. Cell-level functional studies 13. Pathway analysis 14. Next generation sequencing 15. OMIM or disease DB 16. Comparative genomics 17. Technologies unknown yet

How: Define each question in terms of biologists’ interests. Describe the limits of each question. Find the best or second best tools for each question. How to combine the questions for the sake of biologists (input and output data)

Find out the best example of these kind of approaches (ex. SRS of Lions, )

• check  FESD II schema
• check Yamashita-san code for TFBS analysis