This web-site was developed to support these two publications:

Xu H, Ang YS, Sevilla A, Lemischka IR, Ma'ayan A.
Construction and validation of a regulatory network for pluripotency and self-renewal of mouse embryonic stem cells.

PLoS Comput Biol. 2014 Aug 14;10(8):e1003777 | PubMed | single cell and KD followed by RT-PCR data |

Xu H, Baroukh C, Dannenfelser R, Chen EY, Tan CM, Kou Y, Kim YE, Lemischka IR, Ma'ayan A.
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.

Database (Oxford). 2013 Jun 21;2013:bat045 | PubMed |

Please cite these papers if you use the resources available from this website.

Perform enrichment analysis by querying the ESCAPE database.

Download an individual table or the entire ESCAPE database.

Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network.
Yen-Sin Ang, Su-Yi Tsai, Dung-Fang Lee, Jonathan Monk, Jie Su, Kajan Ratnakumar, et al. in Cell (2011)

SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells.
Huilei Xu, Ihor R Lemischka, Avi Ma'ayan in BMC systems biology (2010)

GATE: software for the analysis and visualization of high-dimensional time series expression data.
Ben D MacArthur, Alexander Lachmann, Ihor R Lemischka, Avi Ma'ayan in Bioinformatics (2010)

Systems-level dynamic analyses of fate change in murine embryonic stem cells.
Rong Lu, Florian Markowetz, Richard D Unwin, Jeffrey T Leek, Edoardo M Airoldi, Ben D MacArthur, et al. in Nature (2009)

Systems biology of stem cell fate and cellular reprogramming.
Ben D MacArthur, Avi Ma'ayan, Ihor R Lemischka in Nat Rev Mol Cell Biol (2009)


MATLAB software for learning Boolean transition functions given a directed network.
High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence (ESCAPE) integrating data from many recent diverse high-throughput studies including: gene expression microarrays, RNA-seq, ChIP-chip/seq, genome-wide inhibitory RNA (RNAi) screens, immunoprecipitation followed by mass spectrometry (IP-MS) proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and identify known and novel regulatory interactions across various regulatory layers, as well as predict the effects of combinatorial knockdowns.

Stem cells, systems biology and human feedback
Mount Sinai researchers hope that systems biology can show how molecular processes within a cell control its fate. Lemischka works with his biologist colleagues to perturb gene expression in stem cells. Using the technique of RNA interference, they can remove one transcription factor at a time at time zero, right after cell division, and measure changes such as those in transcription levels for genes over time.
Read more at:

New database could speed up drug discovery
A new database and software, called ChIP Enrichment Analysis, or ChEA, is set to revolutionize how researchers identify drug targets and biomarkers. Until ChEA was developed, no centralized database integrated results from, for instance, ChIP-seq and ChIP-chip experiments (these are used to identify how "transcription factor" proteins might regulate all genes in humans and mice). Now this new computational method should help streamline how scientists analyze these gene expression experiments.