TEISER
Supplementary web site for "Systematic discovery of structural elements governing stability of mammalian messenger RNAs"
Hani Goodarzi, Hamed S. Najafabadi, Panos Oikonomou, Todd M. Greco, Lisa Fish, Reza Salavati, Ileana M. Cristea and Saeed Tavazoie
To contact us: {hgoodarzi@rockefeller.edu, hamed.najafabadi@utoronto.ca, st2744@columbia.edu}
How can I use TEISER?
IGET: Use TEISER online
A limited version of TEISER is available as part of IGET, an integrated platform for exploring large-scale gene expression and protein behavior dynamics. However, we strongly recommend downloading and using TEISER in house as it requires access to multiple nodes and computational power to complete the jobs in a reasonable time.
Use IGET to discover motifs, pathways, and interactions.
TEISER can be downloaded and used as a command line program (on a Unix or Cygwin machine).
TEISER comes with pre-packaged sequence data for a number of organisms:
human (H. sapiens; 5' & 3' UTRs),
mouse (M. musculus; 5' & 3' UTRs),
yeast (S. cerevisiae; upstream & downstream sequences)
If your favorite organism is not in the list and you would like us to add it, please contact us. You can also add your own organisms (see tutorial or contact us for more details).
TEISER (for Tool for Eliciting Informative Structural Elements in RNA) is a robust and powerful framework for discovering post-transcriptional regulatory elemenets. Click here for a tutorial on how to install and use TEISER.
Supplemental results
Discovering post-transcriptional cis-regulatory elements underlying mRNA stability
Input data:
mRNA stability measurements: .txt .xls
Results:
False-discovery rate set at 0.0: .pdf .txt
False-discovery rate set at 0.1: .pdf .txt
Predicted target sites as weight-matrices: .pdf
Non-discovery analysis of experimental results
Decoy vs. scrambled oligos: sRSM1
Expression profiles of decoy-transfected vs. scrambled transfected MDA-MB-231 cells: Set1 Set2
TEISER results (non-discovery mode): Set1 Set2
HNRPA2B1 siRNA knock-down experiments
Expression profiles of siRNA-transfected vs. mock-transfected MDA-MB-231 cells: siRNA1 siRNA2 siRNA3
TEISER results (non-discovery mode): siRNA1 siRNA2 siRNA3
Relative decay rates of siRNA-transfected vs. mock-transfected MDA-MB-231 cells: siRNA pool
TEISER results (non-discovery mode): siRNA pool
HNRPA2B1 RIP-chip
Transcript abundances in HNRPA2B1 immunoprecipitation samples: Replicate1 Replicate2
TEISER results (non-discovery mode): Replicate1 Replicate2
HNRPA2B1 HITS-CLIP
Sequences bound by HNRPA2B1 in vivo: Replicate1 Replicate2
TEISER results (non-discovery mode): Replicate1 Replicate2
CIMS analysis of HNRPA2B1 HITS-CLIP
Sequences bound by HNRPA2B1 in vivo: .fasta
TEISER results (non-discovery mode): .pdf
Examples of crosslinked bindign sites: .pdf
HNRPA2B1 data from Huelga et al. Cell (2012)
HNRPA2B1 siRNA knock-down: data result
HNRPA2B1 HITS-CLIP: Binding sites (real and random) result
Deciphering the post-transcriptional regulatory program underlying mRNA stability
FIRE: Finding linear motifs in addition to TEISER's structural elements
Motif-motif interaction maps
Structural motifs vs. structural motifs (examplary interactions between sRSM0 and other elements): .pdf .txt
Structural motifs vs. linear motifs: .pdf .txt
iPAGE:Finding putative target pathways for the discovered elements
iPAGE results for structural motifs: .pdf .txt
iPAGE results for linear motifs: .pdf .txt
Post-transcriptional Regulatory Program
All discovered dependencies are combined into a single figure.