Meeting Notes

Resources

1. Tools
   • Zlab Gene Regulation Tools
   • MSCAN
   • Meta-MEME v2.1
   • Cis-Analyst
   • Gibbs Motif Sampler Homepage
   • TFBS Modules for Bioperl
2. Public Data Sets
   • Catalogue of Regulatory Elements (Muscle Data by Wasserman and Fickett)
   • Liver model, supplementary material (Krivan)
   • Nucleotide Count Matrices by Martin Frith (Zlab)
   • Regulatory Elements (Compilation by Elnitsky)
   • JASPAR
   • Consite
3. My Extended Data Sets (Updated on Jan. 9, 2004)
   • Original Muscle Data by Wasserman(Human, Rat, Mouse Only)
   • New Muscle Data by Kwon (Human, Rat, Mouse Only)
   • Combined Muscle Data (Human, Rat, Mouse Only) - updated on July 22, 2005
   • Original Liver Data by Krivan(Human, Rat, Mouse Only)
   • New Liver Data by Andrew (Human, Rat, Mouse Only)
   • Combined Liver Data (Human, Rat, Mouse Only)
   • Muscle Test Sequences (Human, Rat, Mouse Only; 1 kb; unmasked and masked)
   • Liver Test Sequences (Human, Rat, Mouse Only; 1 kb; unmasked and masked)
   • Human Negative Sequences (5' 1 kb and 10 kb; unmasked and masked)
   • Mouse Negative Sequences (5' 1 kb and 10 kb; unmasked and masked)
4. Matrix Data
   • PWM for Muscle TFBS (derived from muscle sequences)
   • PWM for Muscle TFBS (derived from non-muscle sequences)
   • PFM for Liver TFBS (used by William Krivan; needs conversion to PWM)