Stemformatics: visualisation and sharing of stem cell gene expression

Wells, Christine A., Mosbergen, Rowland, Korn, Othmar, Choi, Jarny, Seidenman, Nick, Matigian, Nicholas A., Vitale, Alejandra M. and Shepherd, Jill (2013) Stemformatics: visualisation and sharing of stem cell gene expression. Stem Cell Research, 10 3: 387-395. doi:10.1016/j.scr.2012.12.003

Related Publications and Datasets
Author Wells, Christine A.
Mosbergen, Rowland
Korn, Othmar
Choi, Jarny
Seidenman, Nick
Matigian, Nicholas A.
Vitale, Alejandra M.
Shepherd, Jill
Title Stemformatics: visualisation and sharing of stem cell gene expression
Journal name Stem Cell Research   Check publisher's open access policy
ISSN 1873-5061
Publication date 2013-05-01
Year available 2012
Sub-type Article (original research)
DOI 10.1016/j.scr.2012.12.003
Open Access Status DOI
Volume 10
Issue 3
Start page 387
End page 395
Total pages 9
Place of publication Netherlands
Publisher Elsevier
Language eng
Formatted abstract
Genome-scale technologies are increasingly adopted by the stem cell research community, because of the potential to uncover the molecular events most informative about a stem cell state. These technologies also present enormous challenges around the sharing and visualisation of data derived from different laboratories or under different experimental conditions. Stemformatics is an easy to use, publicly accessible portal that hosts a large collection of exemplar stem cell data. It provides fast visualisation of gene expression across a range of mouse and human datasets, with transparent links back to the original studies. One difficulty in the analysis of stem cell signatures is the paucity of public pathways/gene lists relevant to stem cell or developmental biology. Stemformatics provides a simple mechanism to create, share and analyse gene sets, providing a repository of community-annotated stem cell gene lists that are informative about pathways, lineage commitment, and common technical artefacts. Stemformatics can be accessed at

Highlights ► Stemformatics is a repository of highly-curated, high-quality gene expression data. ► Find the expression of your gene of interest in exemplar Stem Cell Datasets ► No prior bioinformatics knowledge needed — easy to use interface, clear graphics ► Looked for shared patterns of expression across different cell types ► Create, save and share gene lists or analyses with collaborators
Keyword Database
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Available online 20 December 2012

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
Australian Institute for Bioengineering and Nanotechnology Publications
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Citation counts: TR Web of Science Citation Count  Cited 18 times in Thomson Reuters Web of Science Article | Citations
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