Rosetta Inpharmatics, Inc.

Merck Sharp + Dohme Corp.

Stewart Scherer

Daniel D Shoemaker

Stephen H Friend

Matthew N Ashby

Steven J Altschuler

Lani Fang Wu

Christopher D Armour

Michael Ziman

John W Phillips

Nicholas Marini

The present invention provides methods for analyzing exon expression profiles of a cell or type of cell. In the invention, the expression levels of a plurality of individual exons or multiexons for each of a plurality of genes in the genome of an organism are measured and analyzed to determine the biological state, such as the exon expression state or transcriptional state, of the cell or type of cell. The methods of the invention are useful for determination of alternative RNA splicing in a plurality of genes. The invention also provides nucleic acid probe arrays for determining in parallel the expression levels of a plurality of exons or multiexons for each of a plurality of genes in the genome of an organism. The invention further provides methods for determining the effects of perturbations, such as perturbations by drugs, on exon expression and alternative RNA splicing pathways.

Compositions and methods for exon profiling

The present invention relates to methods of identifying genes whose expression is indicative of activation of a particular biochemical or metabolic pathway or a common set of biological reactions or functions in a cell ('regulon indicator genes') The present invention provides an example of such an indicator gene. The present invention also relates to methods of partially characterizing a gene of unknown function by determining which biological pathways, reactions or functions its expression is associated with, thereby placing the gene within a functional genetic group or 'regulon'. These partially characterized genes may be used to identify desirable therapeutic targets of biological pathways of interest (&#x201c;regulon target genes&#x201d;) The present invention provides examples of such target genes. Methods for identifying effectors (activators and inhibitors) of regulon target genes are provided. The present invention also provides examples of regulon target gene inhibitors.

Methods for the identification of inhibitors of an isoprenoid metabolic pathway

The invention relates to methods and systems (e.g., computer systems and computer program products) for identifying and characterizing genes using microarrays. In particular, the invention provides for improved, robust methods for detecting genes through the use of microarrays to analyze the expression state of the genome. Genes which are expressed can be mapped to their respective positions in the genome, and the structure of such genes can be determined.

Gene discovery using microarrays

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Moraga, CA, United States of America

Stewart Scherer