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

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.

Evaluating Cell Identity from Transcription Profiles

“…We propose the CellScore method as a freely available method to evaluate any kind of cell identity transition, which could in principle score any type of cell transition for which donor cell and target cell data are available, regardless of the platform. The current study has been limited to data from one platform as a proof-of-principle, but in the future, we aim to leverage the data from additional microarray platforms, as well as RNA-seq datasets, for a comprehensive expression database (Mah et al, 2017) to evaluate cell identity.…”

Stemformatics: visualize and download curated stem cell data

“…Other stem cell transcriptome databases are typically limited to hosting single technological platforms. For example, both StemMapper (2) and CellFinder (3) host datasets generated on the Affymetrix microarray technology. Stemformatics is now on Version 7, which uses Ensembl human genome release 91 (hg38).…”