ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells

Huilei Xu,Edward Y Chen,Caroline Baroukh,Avi Ma'Ayan,Christopher M Tan,Yujin E Kim,Ruth Dannenfelser,Ihor R Lemischka,Yan Kou

doi:10.1093/database/bat045

Huilei Xu, Edward Y Chen + Show 7 more

Open Access

https://doi.org/10.1093/database/bat045

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Journal: Database	Publication Date: Jan 1, 2013
Citations: 100	License type: CC BY 3.0

Affiliation: Icahn School of Medicine at Mount Sinai

Abstract

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 integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community.Database URL: http://www.maayanlab.net/ESCAPE

Highlights

Embryonic stem cells (ESCs) are pluripotent cells characterized by their capability to self-renew and differentiate into all adult cell types
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. Efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind
We present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse highthroughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA

Summary

Introduction

Embryonic stem cells (ESCs) are pluripotent cells characterized by their capability to self-renew and differentiate into all adult cell types. (page number not for citation purposes) web-based interfaces for data query and visualization In general, these databases contain information from a single regulatory layer, mostly transcriptome measurements, and overlook other important layers as well as cross-layer interactions. This database integrates numerous additional types of data ranging from epigenetics, transcriptomics, to proteomics and phosphoproteomics. A rich-content web-based application has been developed to enable users to interact with the various types of data in the ESCAPE database These tools enable users to construct subnetworks, perform enrichment analyses visualized on a canvas and predict lineage specification based on in silico gene KDs or overexpressions

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