Title:
SYSTEMS AND METHODS OF SELECTING COMBINATORIAL COORDINATELY DYSREGULATED BIOMARKER SUBNETWORKS
Document Type and Number:
WIPO Patent Application WO/2011/133834
Kind Code:
A3
Abstract:
Systems and methods of selecting combinatorial coordinately dysregulated biomarker subnetworks are provided. In one embodiment, a method comprises comparing the normalized gene expression data to a predetermined threshold to provide binary gene expression data associated with phenotype samples and control samples, analyzing subnetwork states of the binary gene expression data associated with phenotype samples and control samples to identify gene expression patterns that occur in phenotype samples and do not occur in control samples and identifying a subnetwork that provides gene expression patterns indicative of a sample being a phenotype sample.
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Inventors:
KOYUTURK MEHMET (US)
CHANCE MARK (US)
NIBBE ROD (US)
CHOWDHURY SALIM AKHTER (US)
CHANCE MARK (US)
NIBBE ROD (US)
CHOWDHURY SALIM AKHTER (US)
Application Number:
PCT/US2011/033527
Publication Date:
March 15, 2012
Filing Date:
April 22, 2011
Export Citation:
Assignee:
UNIV CASE WESTERN RESERVE (US)
KOYUTURK MEHMET (US)
CHANCE MARK (US)
NIBBE ROD (US)
CHOWDHURY SALIM AKHTER (US)
KOYUTURK MEHMET (US)
CHANCE MARK (US)
NIBBE ROD (US)
CHOWDHURY SALIM AKHTER (US)
International Classes:
C12Q1/68; G16B20/20; G16B25/10; G16B40/00
Other References:
CHOWDHURY S.A. ET AL.: "Subnetwork state functions define dysregulated subnetworks in cancer", J. COMPUT. BIOL., vol. 18, no. 3, March 2011 (2011-03-01), pages 263 - 281, XP055070319
SCHADT E.E. ET AL.: "An integrative genomics approach to infer causal associations between gene expression and disease", NAT. GENET., vol. 37, no. 7, July 2005 (2005-07-01), pages 710 - 717, XP055070320
CHUANG, H. Y. ET AL.: "Network-based classification of breast cancer metastasis", MOL. SYST. BIOL., vol. 3, 2007, XP002498645
LIU M. ET AL.: "Network-based analysis of affected biological processes in type 2 diabetes models. e96", PLOS GENET., vol. 3, no. 6, June 2007 (2007-06-01), pages 0958 - 0972, XP055070326
RHODES D.R. ET AL.: "Integrative analysis of the cancer transcriptome", NAT. GENET., vol. 37, June 2005 (2005-06-01), pages S31 - S37, XP055070327
SCHADT E.E. ET AL.: "An integrative genomics approach to infer causal associations between gene expression and disease", NAT. GENET., vol. 37, no. 7, July 2005 (2005-07-01), pages 710 - 717, XP055070320
CHUANG, H. Y. ET AL.: "Network-based classification of breast cancer metastasis", MOL. SYST. BIOL., vol. 3, 2007, XP002498645
LIU M. ET AL.: "Network-based analysis of affected biological processes in type 2 diabetes models. e96", PLOS GENET., vol. 3, no. 6, June 2007 (2007-06-01), pages 0958 - 0972, XP055070326
RHODES D.R. ET AL.: "Integrative analysis of the cancer transcriptome", NAT. GENET., vol. 37, June 2005 (2005-06-01), pages S31 - S37, XP055070327
Attorney, Agent or Firm:
SUTKUS, Richard, A. (Sundheim Covell & Tummino LLP,1300 East Ninth Street Suite 170, Cleveland OH, US)
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