CLIP-Seq Analysis of Alternative Exons

CLIP tags and clusters were analyzed with BED or WIG formatted custom tracks using the UCSC Genome Browser and Genome Graph tools (genome.ucsc.edu). Composite maps were generated by determining the distance between tags and closest splice sites within the alternative exon local region and converted to coordinates in a BED format custom track, with tags from each gene assigned different colors. MEME sequence analysis was done using tools available at meme.sdsc.edu. ASPIRE2 was based on ASPIRE20 (link).

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Licatalosi D.D., Mele A., Fak J.J., Ule J., Kayikci M., Chi S.W., Clark T.A., Schweitzer A.C., Blume J.E., Wang X., Darnell J.C, & Darnell R.B. (2008). HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature, 456(7221), 464-469.

Publication 2008

Alternative splice sites Clip Exon Gene Genome Maps Sequence analysis

Corresponding Organization :

Other organizations : Howard Hughes Medical Institute, MRC Laboratory of Molecular Biology, Rockefeller University, Biocom

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Variable analysis

independent variables

CLIP tags and clusters were analyzed with BED or WIG formatted custom tracks using the UCSC Genome Browser and Genome Graph tools
Composite maps were generated by determining the distance between tags and closest splice sites within the alternative exon local region
MEME sequence analysis was done using tools available at meme.sdsc.edu
ASPIRE2 was based on ASPIRE20

dependent variables

Measured outcomes

control variables

Kept constant to ensure valid results

controls

Positive controls not explicitly mentioned
Negative controls not explicitly mentioned

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