Time-courses analysis overview
Here you find a description of the analyses applied consistently to all (or certain classes of) time-courses. Follow the links in this overview page to get to the detailed descriptions.
Analysis providers: please edit this page to establish downstream pages detailing your analysis.
Quality control with a set of basic analyses (Erik Arner's analysis)
DPI clustering (Hideya Kawaji)
TSS classifier (Timo Lassmann)
Novel motifs in time-courses (Vsevolod Makeev, Ivan Kulakovskiy, Ulf Schaefer, Yulia Medvedeva, Michael Rehli)
Expression analysis by CAGE (Break don to smaller items her? Or establish many sub-pages). (Erik Arner, Owen Rackham, Sarah, Wyeth Wasserman, Anthony Mathelier, Boris Lenhard, Vanja Haberle, Finn Drablos, Morten Rye, Carlo Cannistraci, Tim Ravasi, Kim-Anh Le Cao, others)
Enhancers and their RNA (Albin et al.)
Alternative promoters (Emmanuel Dimont; Martin Taylor, Sarah Baker)
MARA (Erik van Nimwegen, Peter Pemberton-Ross, Erik Arner)
Genome variation and expression (Kenneth Baillie)
miRNA (Erik Arner, Pal Saetrom, others)
Other topics (establish page yourself):
- TF analysis expression, TF based network
- TF that characterize a given cellular state (and drive it?);
- TF and diseases literature search
- Biolayout to all samples
- Antisense promoters
- Enhancers connection to target (Hi-C, Chia-PET. Etc.)
- SNP of each promoter, enhancer, ncRNAs at each isolated key feature in time courses
- Noncoding RNA: long and small; including Retrotransposon elements expression
- The above non-coding RNA that characterize a cellular state
- Retrotransposons retrotransposition (targeted RE capture)
- Antisense and ncRNAs associated to TF and other protein coding RNAs
- ncRNAs that show up in specific time course points, candidate for specific validation
- Seed for future mechanistic studies by each laboratory
- Human versus mouse, data analysis for both systems
- Concordant-discordant promoters in the time course (within time course; what is their biology)
- Ripple of transcription (and what is the relation with enhancer?)
