NDLI: Emergent Genome-Wide Control in Wildtype and Genetically Mutated Lipopolysaccarides-Stimulated Macrophages

Content Provider	PubMed Central
Author	Tsuchiya, Masa Piras, Vincent Choi, Sangdun Akira, Shizuo Tomita, Masaru Giuliani, Alessandro Selvarajoo, Kumar
Editor	Sommer, Peter
Copyright Year	2009
Abstract	Large-scale gene expression studies have mainly focused on highly expressed and ‘discriminatory’ genes to decipher key regulatory processes. Biological responses are consequence of the concerted action of gene regulatory network, thus, limiting our attention to genes having the most significant variations is insufficient for a thorough understanding of emergent whole genome response. Here we comprehensively analyzed the temporal oligonucleotide microarray data of lipopolysaccharide (LPS) stimulated macrophages in 4 genotypes; wildtype, Myeloid Differentiation factor 88 (MyD88) knockout (KO), TIR-domain-containing adapter-inducing interferon-β (TRIF) KO and MyD88/TRIF double KO (DKO). Pearson correlations computed on the whole genome expression between different genotypes are extremely high (>0.98), indicating a strong co-regulation of the entire expression network. Further correlation analyses reveal genome-wide response is biphasic, i) acute-stochastic mode consisting of small number of sharply induced immune-related genes and ii) collective mode consisting of majority of weakly induced genes of diverse cellular processes which collectively adjust their expression level. Notably, temporal correlations of a small number of randomly selected genes from collective mode show scalability. Furthermore, in collective mode, the transition from large scatter in expression distributions for single ORFs to smooth linear lines emerges as an organizing principle when grouping of 50 ORFs and above. With this emergent behavior, the role of MyD88, TRIF and novel MyD88, TRIF-independent processes for gene induction can be linearly superposed to decipher quantitative whole genome differential control of transcriptional and mRNA decay machineries. Our work demonstrates genome-wide co-regulated responses subsequent to specific innate immune stimulus which have been largely neglected.
Related Links	http://dx.doi.org/10.1371/journal.pone.0004905
Starting Page	4905
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	3
Volume Number	4
Language	English
Publisher	Public Library of Science
Publisher Date	2009-03-20
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Emergent Genome-Wide Control in Wildtype and Genetically Mutated Lipopolysaccarides-Stimulated Macrophages

Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages

Integrative Genome-Wide Expression Analysis Bears Evidence of Estrogen Receptor-Independent Transcription in Heregulin-Stimulated MCF-7 Cells

Genome-Wide and Locus Specific Alterations in CDC73/HRPT2-Mutated Parathyroid Tumors

Glucose Controls Morphodynamics of LPS-Stimulated Macrophages

Accumulation of Wildtype and ALS-Linked Mutated VAPB Impairs Activity of the Proteasome

TEX11 is mutated in infertile men with azoospermia and regulates genome-wide recombination rates in mouse

NMD Microarray Analysis for Rapid Genome-Wide Screen of Mutated Genes in Cancer

Genome-wide polysomal analysis of a yeast strain with mutated ribosomal protein S9

Emergent Genome-Wide Control in Wildtype and Genetically Mutated Lipopolysaccarides-Stimulated Macrophages

Similar Documents

Emergent Genome-Wide Control in Wildtype and Genetically Mutated Lipopolysaccarides-Stimulated Macrophages

Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages

Integrative Genome-Wide Expression Analysis Bears Evidence of Estrogen Receptor-Independent Transcription in Heregulin-Stimulated MCF-7 Cells

Genome-Wide and Locus Specific Alterations in CDC73/HRPT2-Mutated Parathyroid Tumors

Glucose Controls Morphodynamics of LPS-Stimulated Macrophages

Accumulation of Wildtype and ALS-Linked Mutated VAPB Impairs Activity of the Proteasome

TEX11 is mutated in infertile men with azoospermia and regulates genome-wide recombination rates in mouse

NMD Microarray Analysis for Rapid Genome-Wide Screen of Mutated Genes in Cancer

Genome-wide polysomal analysis of a yeast strain with mutated ribosomal protein S9

Emergent Genome-Wide Control in Wildtype and Genetically Mutated Lipopolysaccarides-Stimulated Macrophages