CellFinder's Molecular Database and its Application to Stem Cell Research

Andreas Kurtz,Harald Stachelscheid,Khadija El Amrani,Nancy Mah,Weiping Zhang

doi:10.18547/gcb.2017.vol3.iss1.e48

Andreas Kurtz, Harald Stachelscheid + Show 3 more

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https://doi.org/10.18547/gcb.2017.vol3.iss1.e48

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Abstract

CellFinder is a freely available on-line resource for cell-based data in mammalian cells and in vitro cell lines. CellFinder was developed to provide easier access to different types of cell-based data, which include anatomical and microscopic images, protein expression and whole genome mRNA expression profiles. In this short communication, we describe the collection, processing and storage of gene expression data for the CellFinder resource. Studies involving the use of normal cells and/or production of pluripotent stem cells or their engineered cell types, were chosen from public data repositories of mRNA expression data. Samples in each study were manually curated with ontology terms, and the data was further processed to yield normalized expression data. Sample, experiment and molecular data were stored in a postgreSQL database. The resulting molecular database currently contains 1588 samples from 56 studies, covering 42 cell types in human and mouse. The molecular database is undergoing continuous development and will serve as a source of standardized, processed and expertly annotated data for CellFinder analysis tools such as MarkerTool and CompareTool.

Highlights

METHODSThe CellFinder data repository was initiated in 2004 [1] as comprehensive resource for data used to characterize mammalian cells in tissues over different developmental stages
With the wide availability of transcriptome data in public repositories such as Gene Expression Omnibus and ArrayExpress, there is a large body of data to draw upon for meta-analysis
Like CellFinder, contemporary web resources, such as SHOGoiN/CELLPEDIA [10] and Stemformatics [11], compile cell-based ’-omics’ data from public repositories, but only the former associates its data to ontology terms

Summary

Introduction

METHODSThe CellFinder data repository was initiated in 2004 [1] as comprehensive resource for data used to characterize mammalian cells in tissues over different developmental stages (www.cellfinder.org). Cell-based data; database; web resource; pluripotent stem cells; engineered cell types To facilitate querying of cell-based data, we are manually annotating a selection of microarray datasets with ontology terms from the CellFinder resource.

Results

Conclusion