April 2012

Cover story: Valid -omics data

Moving ahead
Experts in this story all cited the volume of -omics data as a cause of concern for validation. But Matthias Mann of the Max Planck Institute of Biochemistry in Germany is hopeful that the data volume issue will someday be more manageable. Right now, the data volume is an indication of the complexity of biology, but some of the complexity of biology comes from interconnections between different molecular pathways, cells, tissues and organs. “I think we will see in the future that many of the biological changes are not independent of each other but they go together,” he says. “That means the dimensionality of what we are measuring is actually lower … That inherently reduces the complexity.” But he cautions, “Until we know more and have mapped it all out, we will be swimming” in data.

The boundaries of biomedical science can’t be pushed forward without proper validation steps, which have to be integrated in all stages from fundamental research to clinical trials and population studies, say Ioannidis and Khoury. Aebersold points out that researchers suffer from lost money, resources and time if they chase mirages in data. And the repercussions of improper validation are magnified if research has medical applications. As Evans puts it, “You get validation wrong, and people will literally suffer.”

References
  1. 1. Ioannidis, J.P.A. & Khoury, M.J. Science 334, 1230 – 1232 (2011).
  2. 2. (2011) NLM Tech. Bull. 378, e15. NCBI To Discontinue Sequence Read Archive and Peptidome. http://www.nlm.nih.gov/pubs/techbull/jf11/jf11_ncbi_reprint_sra.html.

Raj_MukhopadhyayRajendrani Mukhopadhyay (rmukhopadhyay@asbmb.org) is the senior science writer for ASBMB Today and the technical editor for the Journal of Biological Chemistry.

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A genome, organized into chromosomes that are condensed into nucleosomes, is expressed by the action of enhanceosomes, transcriptosomes and splicosomes as a transcriptome, and with the help of ribosomes the transcriptome is turned into a proteome. Chromosomes, consisting mostly of autosomes, but also X and Y chromosomes, are duplicated by a replisome. Members of the proteome are organized in higher order structures such as peroxisomes, lysosomes, endosomes, etc. Undesirable members of the proteome are attacked by proteasomes (degradomes). Syndromes arise when specific members of the proteome are absent or misbehave. A large number of metabolomes are responsible for providing the required energy and raw materials, while signalosomes or kinomes regulate the creation of order out of chaos. Under certain conditions, constituents of the signalosome activate the apoptosome to organize the return to chaos. Somewhere in all of this MITOCHONDRIA play an absolutely essential role. Immo Scheffler

 

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