Inferring regulatory networks by combining perturbation screens and steady state gene expression profiles.

Inferring regulatory networks by combining perturbation screens and steady state gene expression profiles.

Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction problem. However, such data can be limited in size and/or a...

Full description

Bibliographic Details
Main Authors:	Ali Shojaie, Alexandra Jauhiainen, Michael Kallitsis, George Michailidis
Format:	Article
Language:	English
Published:	Public Library of Science (PLoS) 2014-01-01
Series:	PLoS ONE
Online Access:	http://europepmc.org/articles/PMC3938831?pdf=render

Similar Items

Integration of steady-state and temporal gene expression data for the inference of gene regulatory networks.
by: Yi Kan Wang, et al.
Published: (2013-01-01)

Inference of SNP-Gene Regulatory Networks by Integrating Gene Expressions and Genetic Perturbations
by: Dong-Chul Kim, et al.
Published: (2014-01-01)

Inferring perturbation profiles of cancer samples
by: Beerenwinkel, N., et al.
Published: (2021)

Perturbation theory for open quantum systems at the steady state
by: Edgar A. Gómez, et al.
Published: (2018-09-01)

Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures.
by: Jin Gu, et al.
Published: (2013-01-01)

Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms
by: Daniel Morgan, et al.
Published: (2020-08-01)

An investigation in stem cells in steady state and perturbed intestinal epithelium
by: Gândara, Ricardo Miguel da Cruz
Published: (2011)

Repeated small perturbation approach reveals transcriptomic steady states.
by: Ching-Lung Huang, et al.
Published: (2011-01-01)

Inference of gene regulatory networks from genetic perturbations with linear regression model.
by: Zijian Dong, et al.
Published: (2013-01-01)

Steady-State-Preserving Simulation of Genetic Regulatory Systems
by: Ruqiang Zhang, et al.
Published: (2017-01-01)

Inference of gene regulatory networks with sparse structural equation models exploiting genetic perturbations.
by: Xiaodong Cai, et al.
Published: (2013-01-01)

Stable Gene Regulatory Network Modeling From Steady-State Data
by: Joy Edward Larvie, et al.
Published: (2016-04-01)

The application of perturbation method to problem of misaligned tube in conditions of steady-state creep
by: A. D. Moskalik
Published: (2013-12-01)

A comparative study of topology-based pathway enrichment analysis methods
by: Jing Ma, et al.
Published: (2019-11-01)

Scalable steady state analysis of Boolean biological regulatory networks.
by: Ferhat Ay, et al.
Published: (2009-12-01)

On the transient and steady-state estimates of interval genetic regulatory networks
by: Li, Ping, et al.
Published: (2010)

STRONGLY CONNECTED COMPONENTS AND STEADY STATES IN GENE REGULATORY NETWORKS
by: MILES, RICHARD BRENT
Published: (2007)

Gene regulatory network inference from multifactorial perturbation data using both regression and correlation analyses.
by: Jie Xiong, et al.
Published: (2012-01-01)

Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference
by: Delphine Potier, et al.
Published: (2014-12-01)

Inferring Drug-Target Interactions Based on Perturbational Profiles in LINCS L1000 Data
by: Pei-Han Liao, et al.
Published: (2018)

Perturbation stability for approximate MAP inference
by: Lang, Hunter(Hunter J.)
Published: (2019)

Analysis of steady and perturbed laminar diffusion flames with real kinetics
by: Allison, R. A.
Published: (1978)

Inferring Drosophila gap gene regulatory network: pattern analysis of simulated gene expression profiles and stability analysis
by: Kaandorp Jaap A, et al.
Published: (2009-12-01)

Characterizing the relationship between steady state and response using analytical expressions for the steady states of mass action models.
by: Paul Michael Loriaux, et al.
Published: (2013-01-01)

Ensemble inference and inferability of gene regulatory networks.
by: S M Minhaz Ud-Dean, et al.
Published: (2014-01-01)

State of the Art of Fuzzy Methods for Gene Regulatory Networks Inference
by: Tuqyah Abdullah Al Qazlan, et al.
Published: (2015-01-01)

Antibody-targeting of steady state dendritic cells induces tolerance mediated by regulatory T cells
by: Karsten eMahnke, et al.
Published: (2016-02-01)

Steady-state analysis of nonlinear networks.
by: Agnew, David George
Published: (2011)

Steady state analysis of piping networks
by: Goodman, George Charles
Published: (2005)

Fuzzy Tuning of Combined PID and Steady-State Feedforward Controllers
by: Huang, Wen Sheng, et al.
Published: (1993)

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast.
by: Zhuo Wang, et al.
Published: (2017-05-01)

DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks.
by: Daifeng Wang, et al.
Published: (2016-10-01)

KCML: a machine‐learning framework for inference of multi‐scale gene functions from genetic perturbation screens
by: Heba Z Sailem, et al.
Published: (2020-03-01)

INFERRING OF REGULATORY NETWORKS FROM EXPRESSION DATA USING BAYESIAN NETWORKS
by: Alexander A. Loboda, et al.
Published: (2020-12-01)

Analysis of the steady state hot deformation of aluminum
by: Barclay, George Allan
Published: (2011)

Steady state visual evoked potential (SSVEP) based brain-computer interface (BCI) performance under different perturbations.
by: Zafer İşcan, et al.
Published: (2018-01-01)

Steady-state calcium efflux from aplysia neurons: Perturbation by H202 and protection by stress protein, HSP70
by: Smith, P.J.S, et al.
Published: (1993)

Classification of Cancer and Inference of Cancer-specific Gene Regulatory Networks Based on Gene Expression Profiles Using Soft Computing Rules
by: Wang, Xiaosheng
Published: (2010)

Lac Operon Expression in Steady State Cells of Escherichia coli
by: Cho, SungAe
Published: (1985)

New Necessary Conditions for the Well-Posedness of Steady Bioconvective Flows and Their Small Perturbations
by: Aníbal Coronel, et al.
Published: (2021-08-01)