Motif-based analysis of large nucleotide data sets using MEME-ChIP.
MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can analyze peak regions identified by ChIP-seq, cross-linking sites identified by CLIP-seq and related assays, as well as sets of genomic regions selected using other criteria. MEME-ChIP performs de novo motif discovery, motif enrichment analysis, motif location analysis and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. MEME-ChIP performs two complementary types of de novo motif discovery: weight matrix-based discovery for high accuracy; and word-based discovery for high sensitivity. Motif enrichment analysis using DNA or RNA motifs from human, mouse, worm, fly and other model organisms provides even greater sensitivity. MEME-ChIP's interactive HTML output groups and aligns significant motifs to ease interpretation. This protocol takes less than 3 h, and it provides motif discovery approaches that are distinct and complementary to other online methods.
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
Wenxiu
W
Ma
1] Department of Genome Sciences, University of Washington, Seattle, Washington, USA. [2] Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA.
William S
WS
Noble
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
Timothy L
TL
Bailey
D000465:Algorithms; D001665:Binding Sites / Q000235:genetics*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D016000:Cluster Analysis; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D059372:Nucleotide Motifs / Q000235:genetics*; D012984:Software