Columbia University in the City of New York

Tavazoie Lab


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: {,,}


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


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


Transcript abundances in HNRPA2B1 immunoprecipitation samples: Replicate1 Replicate2

TEISER results (non-discovery mode): Replicate1 Replicate2


Sequences bound by HNRPA2B1 in vivo: Replicate1 Replicate2

TEISER results (non-discovery mode): Replicate1 Replicate2


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

FIRE results: .pdf .txt

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.

© 2011 Columbia University