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Title: Method to determine transcriptional regulation pathways in organisms

Abstract

The invention relates to computer-implemented methods and systems for identifying regulatory relationships between expressed regulating polypeptides and targets of the regulatory activities of such regulating polypeptides. More specifically, the invention provides a new method for identifying regulatory dependencies between biochemical species in a cell. In particular embodiments, provided are computer-implemented methods for identifying a regulatory interaction between a transcription factor and a gene target of the transcription factor, or between a transcription factor and a set of gene targets of the transcription factor. Further provided are genome-scale methods for predicting regulatory interactions between a set of transcription factors and a corresponding set of transcriptional target substrates thereof.

Inventors:
; ; ;
Issue Date:
Research Org.:
Boston University (Boston, MA)
Sponsoring Org.:
USDOE
OSTI Identifier:
1080438
Patent Number(s):
8306752
Application Number:
12/271,944
Assignee:
Trustees of Boston University (Boston, MA)
Patent Classifications (CPCs):
G - PHYSICS G16 - INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS G16B - BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
DOE Contract Number:  
FG02-04ER63803
Resource Type:
Patent
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Gardner, Timothy S., Collins, James J., Hayete, Boris, and Faith, Jeremiah. Method to determine transcriptional regulation pathways in organisms. United States: N. p., 2012. Web.
Gardner, Timothy S., Collins, James J., Hayete, Boris, & Faith, Jeremiah. Method to determine transcriptional regulation pathways in organisms. United States.
Gardner, Timothy S., Collins, James J., Hayete, Boris, and Faith, Jeremiah. Tue . "Method to determine transcriptional regulation pathways in organisms". United States. https://www.osti.gov/servlets/purl/1080438.
@article{osti_1080438,
title = {Method to determine transcriptional regulation pathways in organisms},
author = {Gardner, Timothy S. and Collins, James J. and Hayete, Boris and Faith, Jeremiah},
abstractNote = {The invention relates to computer-implemented methods and systems for identifying regulatory relationships between expressed regulating polypeptides and targets of the regulatory activities of such regulating polypeptides. More specifically, the invention provides a new method for identifying regulatory dependencies between biochemical species in a cell. In particular embodiments, provided are computer-implemented methods for identifying a regulatory interaction between a transcription factor and a gene target of the transcription factor, or between a transcription factor and a set of gene targets of the transcription factor. Further provided are genome-scale methods for predicting regulatory interactions between a set of transcription factors and a corresponding set of transcriptional target substrates thereof.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2012},
month = {11}
}

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Works referenced in this record:

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context
journal, March 2006


Mutual Information Relevance Networks: Functional Genomic Clustering Using Pairwise Entropy Measurements
conference, August 2013