BioMed Central Blog
MEM – a useful tool for searching microarray data
Over recent years the use of microarrays has generated vast amounts of gene expression data. However, these data are not readily accessible, particularly if you want to compare data from different studies. In a paper just published in Genome Biology, Jaak Vilo and colleagues at the University of Tartu, Estonia, have come up with a potential solution for this. They have assembled all microarray datasets in the ArrayExpress database and compiled them into a single, searchable database, allowing researchers to search for the expression of a given gene across all experiments and conditions, including in mouse as well as human. The package (called Multi Experiment Matrix, or MEM) then returns all genes significantly co-expressed with the query gene. The software package is intuitive and easy to use and potentially opens up a vast mine of largely unexplored data for researchers to exploit.
Read the article here.
MEM is freely available and can be accessed here.
Posted by Andrew Cosgrove at 15:14 Comments (0)
Can plausibility be quantified?
As the probability of a specific occurrence or outcome tends towards 0 it becomes less likely, but even the most unlikely events rarely attain classification as an absolute impossibility. However, there appears to be a need to address the misunderstanding that theoretical possibility is the same as plausibility, if only to save the funds spent, and the subsequent time of peer reviewers, on research that pushes the boundaries of credibility.
A solution to this problem has recently been proposed in an article published in Theoretical Biology & Medical Modelling. Dr Abel draws upon previous descriptions and concepts in his article The Universal Plausibility Metric (UPM) & Principle (UPP) and describes an equation, featuring the pre-defined concepts of UPM and UPP, to determine the threshold for implausibility and suggests that it should be used to assess the plausibility of a hypothesis as part of the methods for future research.
Although the biggest impact of this application would be within the fields of astrobiology and life-origin research, it could be applied in all fields of scientific investigation.
Should this equation be used to identify whether a hypothesis is too far-fetched to justify scientific expenditure and investigation? Or do we have a need to test the nigh on impossible in order to satisfy curiosity and to continue to delve into the unknown and improbable?
Posted by Lisa Phelps at 11:11 Comments (0)