Pathway and gene-set activation measurement from mRNA expression data the tissue distribution of human pathways 英文参考文献.docVIP
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Pathway and gene-set activation measurement from mRNA expression data the tissue distribution of human pathways 英文参考文献
Open Access
Re rch
2006LevineetVoal.lumesea7, Issue 10, Article R93
Pathway and gene-set activation measurement from mRNA
expression data: the tissue distribution of human pathways
David M Levine*, David R Haynor?, John C Castle*, Sergey B Stepaniants*,
Matteo Pellegrini?, Mao Mao* and Jason M Johnson*
Addresses: *Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck and Co., Inc., Terry Avenue North, Seattle, WA 98109, USA.
?Department of Radiology, University of Washington, Seattle, WA 98195, USA. ?Department of MCD Biology, University of California at Los
Angeles, Los Angeles, CA 90095, USA.
Correspondence: Jason M Johnson. Email: jason_johnson@
Published: 17 October 2006
Received: 12 July 2006
Revised: 13 September 2006
Accepted: 17 October 2006
Genome Biology 2006, 7:R93 (doi:10.1186/gb-2006-7-10-r93)
The electronic version of this article is the complete one and can be
found online at /2006/7/10/R93
? 2006 Levine et al.; licensee BioMed Central Ltd.
This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which
permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
ThesepntAetissuedc.om/ppdistributionarison of fivofe dhumanifferentpathwaysmeasures of pathway expression and a public map of pathway expression in human tissues are pre-
Abstract
Background: Interpretation of lists of genes or proteins with altered expression is a critical and
time-consuming part of microarray and proteomics research, but relatively little attention has been
paid to methods for extracting biological meaning from these output lists. One powerful approach
is to examine the expression of predefined biological pathways and gene sets, such as metabolic
and signaling pathways and macromolecular complexes. Although many methods for measuring
pathway expression have been proposed, a systematic analysis of the per
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