WO2013040076A1 - Dynamique et contrôle des réseaux liés à l'état permettant d'explorer une organisation génomique - Google Patents

Dynamique et contrôle des réseaux liés à l'état permettant d'explorer une organisation génomique Download PDF

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Publication number
WO2013040076A1
WO2013040076A1 PCT/US2012/054921 US2012054921W WO2013040076A1 WO 2013040076 A1 WO2013040076 A1 WO 2013040076A1 US 2012054921 W US2012054921 W US 2012054921W WO 2013040076 A1 WO2013040076 A1 WO 2013040076A1
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Prior art keywords
network
state
cell
transcriptional
controllability
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PCT/US2012/054921
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English (en)
Inventor
Indika RAJAPAKSE
Mark Groudine
Mehran MESBAHI
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Fred Hutchinson Cancer Research Center
University Of Washington Through Its Center For Commercialization
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Application filed by Fred Hutchinson Cancer Research Center, University Of Washington Through Its Center For Commercialization filed Critical Fred Hutchinson Cancer Research Center
Publication of WO2013040076A1 publication Critical patent/WO2013040076A1/fr

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    • 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
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks

Definitions

  • FIGURE 5 illustrates a pictorial diagram in accordance with various embodiments of the present subject matter
  • Hi-C a method that probes the three-dimensional architecture of whole genomes by coupling cross-linking of chromosomal sites with massively parallel sequencing.
  • spatial proximity maps of the human genome were constructed at a resolution of 0.1-1.0 megabase pairs in two human hematopoietic cell lines representing distinct hematopoietic lineages, one derived from B-lymphocytes and the other an erythroleukemia-derived line.
  • GATA-1 Another "master regulator” is GATA-1, a zinc finger transcription factor essential to maintenance of the erythroid and megakaryocyte lineages.
  • GATA-1 may have a global impact on nuclear organization by catalyzing interactions within and among the coregulated gene and chromosome topology networks.
  • Others have used ChiP-Seq methods to identify the spatial distribution of ds-regulatory elements targeted by GATA-1, and they determine criteria for distinguishing between target sites that promote activation versus repression of genes during erythroid development. The broad influence of these transcription factors provides a platform for understanding control over development of specific cell types.
  • the proposed framework may also help identify previously uncharacterized master regulators that globally influence cell fate.
  • controllability Gramian is defined as the solution of the Lyapunov equation
  • the differential entropy is ln(a - b).
  • the uniformly minimum variance unbiased entropy estimate for the Gaussian is,
  • the distance D can be extended to the case where Wis singular as follows: where a and b are now r x 1.
  • N(A) denote, respectively, its range space and null space.
  • a matrix and/or a vector that consists of all zero entries will be denoted by 0; whereas, '0' will simply denote the scalar zero.
  • p 2, ⁇
  • ⁇ S ⁇ denotes its cardinality.
  • An undirected (simple) graph G is specified by a vertex set G and an edge set G whose elements characterize the incidence relation between distinct pairs of G.
  • incidence matrix is pervasive including

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  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Physiology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)

Abstract

L'invention concerne un procédé exécutable par ordinateur permettant de caractériser la contrôlabilité d'un réseau ainsi que des nœuds influents dans un réseau par une entropie du réseau au moyen d'un ou de plusieurs dispositifs informatiques. Le procédé est particulièrement utile pour les réseaux liés à l'état, tels que le génome d'une cellule, dans lesquels la géométrie chromosomique est directement liée à l'activité génomique, qui a son tour est étroitement corrélée avec la géométrie. Actuellement, il n'existe pas de méthodologie systématique permettant d'évaluer la contrôlabilité d'un réseau à partir de mesures expérimentales. L'invention fournit une telle technique d'évaluation et d'analyse exécutable par ordinateur pour examiner la contrôlabilité du réseau et classer les configurations réseau critiques qui sont susceptibles de subir une influence externe. Le procédé fournit un moyen exécutable par ordinateur permettant de ne pas identifier uniquement un état de réception dans la cellule, mais également plusieurs nouvelles cibles dans un système pathologique de façon simultanée. Le procédé est également utile et possède des applications permettant de concevoir des mécanismes d'influence, par ex. des stratégies de marketing sur des réseaux sociaux, de concevoir des stratégies de vaccination pour influencer la progression d'une maladie infectieuse, et de concevoir des réseaux robotiques solides, par ex. ceux qui sont moins contrôlables par rapport aux perturbations externes.
PCT/US2012/054921 2011-09-12 2012-09-12 Dynamique et contrôle des réseaux liés à l'état permettant d'explorer une organisation génomique WO2013040076A1 (fr)

Applications Claiming Priority (2)

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US201161533776P 2011-09-12 2011-09-12
US61/533,776 2011-09-12

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WO2013040076A1 true WO2013040076A1 (fr) 2013-03-21

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Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN104778173A (zh) * 2014-01-10 2015-07-15 腾讯科技（深圳）有限公司 目标用户确定方法、装置及设备
US10594642B2 (en) 2017-01-03 2020-03-17 International Business Machines Corporation Responding to an electronic message communicated to a large audience
CN112462779A (zh) * 2020-11-30 2021-03-09 汕头大学 基于基因调控网络的群体机器人动态围捕控制方法及系统
CN115295072A (zh) * 2022-10-10 2022-11-04 山东大学 基于图神经网络的蛋白质相互作用位点预测方法及系统
WO2023150898A1 (fr) * 2022-02-08 2023-08-17 Chromatintech Beijing Co, Ltd Procédé d'identification d'une caractéristique structurale de la chromatine à partir de la matrice hi-c, moyen non transitoire lisible par ordinateur stockant un programme d'identification d'une caractéristique structurale de la chromatine à partir de la matrice hic

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5615319A (en) * 1992-01-16 1997-03-25 Hewlett-Packard Company Method for modifying a geometric object and computer aided design system
EP1540505A2 (fr) * 2002-08-29 2005-06-15 Gene Network Sciences, Inc. Systemes et procedes de deduction de reseaux biologiques
EP1764717A1 (fr) * 2004-06-25 2007-03-21 National Institute of Advanced Industrial Science and Technology Système d'analyse de réseau de cellules
WO2009038248A1 (fr) * 2007-09-21 2009-03-26 Electronics And Telecommunications Research Institute Appareil et procédé pour visualiser l'état d'un réseau en utilisant des informations géographiques

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5615319A (en) * 1992-01-16 1997-03-25 Hewlett-Packard Company Method for modifying a geometric object and computer aided design system
EP1540505A2 (fr) * 2002-08-29 2005-06-15 Gene Network Sciences, Inc. Systemes et procedes de deduction de reseaux biologiques
EP1764717A1 (fr) * 2004-06-25 2007-03-21 National Institute of Advanced Industrial Science and Technology Système d'analyse de réseau de cellules
WO2009038248A1 (fr) * 2007-09-21 2009-03-26 Electronics And Telecommunications Research Institute Appareil et procédé pour visualiser l'état d'un réseau en utilisant des informations géographiques

Cited By (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN104778173A (zh) * 2014-01-10 2015-07-15 腾讯科技（深圳）有限公司 目标用户确定方法、装置及设备
CN104778173B (zh) * 2014-01-10 2020-01-10 腾讯科技（深圳）有限公司 目标用户确定方法、装置及设备
US10594642B2 (en) 2017-01-03 2020-03-17 International Business Machines Corporation Responding to an electronic message communicated to a large audience
US10601752B2 (en) 2017-01-03 2020-03-24 International Business Machines Corporation Responding to an electronic message communicated to a large audience
CN112462779A (zh) * 2020-11-30 2021-03-09 汕头大学 基于基因调控网络的群体机器人动态围捕控制方法及系统
CN112462779B (zh) * 2020-11-30 2023-07-25 汕头大学 基于基因调控网络的群体机器人动态围捕控制方法及系统
WO2023150898A1 (fr) * 2022-02-08 2023-08-17 Chromatintech Beijing Co, Ltd Procédé d'identification d'une caractéristique structurale de la chromatine à partir de la matrice hi-c, moyen non transitoire lisible par ordinateur stockant un programme d'identification d'une caractéristique structurale de la chromatine à partir de la matrice hic
CN115295072A (zh) * 2022-10-10 2022-11-04 山东大学 基于图神经网络的蛋白质相互作用位点预测方法及系统

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