What is the Compare tool?

The Compare tool gives access to a collection of differential genes and proteins between various cell types. The collection is mainly generated from raw microarray datasets. We have tried to gather arrays from different experiments to be able to compare more groups/cell types together. This approach may suffer from batch effects and results should be taken with care. Microarray data was processed using R/Bioconductor and results from all possible pairwise comparisons between groups of arrays (cell types in a given condition) were stored in a local database. The collection contains also protein expression and RNA-seq datasets. Expression values were retrieved from normalized datasets as RPKM. Comparison of RPKM values between datasets may be directly possible but we recommend to be careful. The web pages allow selection of groups in a given dataset to display significant differential genes or proteins and related plots.

References

NCBI GEO database*
Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A.
NCBI GEO: archive for functional genomics data sets—10 years on Nucleic Acids Res. 2011 Jan;39(Database issue):D1005-10

* please use provided Accession identifiers to cite individual studies.

The Human Protein Atlas
Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, Wernerus H, Björling L, Ponten F. Towards a knowledge-based Human Protein Atlas.
Nat Biotechnol. 2010 28(12):1248-50.
PubMed: 21139605
DOI: 10.1038/nbt1210-1248

RNAseq atlas
Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A. RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing. Bioinformatics. 2012 Apr 15;28(8):1184-5. Epub 2012 Feb 17. PubMed PMID: 22345621.

R/Bioconductor
R Development Core Team (2010). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.

Bioconductor: Open software development for computational biology and bioinformatics R. Gentleman, V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, and others 2004, Genome Biology, Vol. 5, R80