Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Democratizing systems immunology with modular transcriptional repertoire analyses.

ABSTRACT: Individual elements that constitute the immune system have been characterized over the few past decades, mostly through reductionist approaches. The introduction of large-scale profiling platforms has more recently facilitated the assessment of these elements on a global scale. However, the analysis and the interpretation of such large-scale datasets remains a challenge and a barrier for the wider adoption of systems approaches in immunological and clinical studies. In this Innovation article, we describe an analytical strategy that relies on the a priori determination of co-dependent gene sets for a given biological system. Such modular transcriptional repertoires can in turn be used to simplify the analysis and the interpretation of large-scale datasets, and to design targeted immune fingerprinting assays and web applications that will further facilitate the dissemination of systems approaches in immunology.

SUBMITTER: Chaussabel D

PROVIDER: S-EPMC4118927 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Democratizing systems immunology with modular transcriptional repertoire analyses.

Chaussabel Damien D Baldwin Nicole N

Nature reviews. Immunology 20140401 4

Individual elements that constitute the immune system have been characterized over the few past decades, mostly through reductionist approaches. The introduction of large-scale profiling platforms has more recently facilitated the assessment of these elements on a global scale. However, the analysis and the interpretation of such large-scale datasets remains a challenge and a barrier for the wider adoption of systems approaches in immunological and clinical studies. In this Innovation article, w ...[more]

PMID: 24662387

Similar Datasets

Opportunities and Challenges in Democratizing Immunology Datasets.

Project description:The field of immunology is rapidly progressing toward a systems-level understanding of immunity to tackle complex infectious diseases, autoimmune conditions, cancer, and beyond. In the last couple of decades, advancements in data acquisition techniques have presented opportunities to explore untapped areas of immunological research. Broad initiatives are launched to disseminate the datasets siloed in the global, federated, or private repositories, facilitating interoperability across various research domains. Concurrently, the application of computational methods, such as network analysis, meta-analysis, and machine learning have propelled the field forward by providing insight into salient features that influence the immunological response, which was otherwise left unexplored. Here, we review the opportunities and challenges in democratizing datasets, repositories, and community-wide knowledge sharing tools. We present use cases for repurposing open-access immunology datasets with advanced machine learning applications and more.

| S-EPMC8086961 | biostudies-literature

Systems immunology analyses of PRRSV

Project description:Transcriptomic analyses of PBMC from PRRSV infected and vaccinated pigs.

| PRJEB47066 | ENA

Modular transcriptional repertoire and MicroRNA target analyses characterize genomic dysregulation in the thymus of Down syndrome infants.

Project description:Trisomy 21-driven transcriptional alterations in human thymus were characterized through gene coexpression network (GCN) and miRNA-target analyses. We used whole thymic tissue--obtained at heart surgery from Down syndrome (DS) and karyotipically normal subjects (CT)--and a network-based approach for GCN analysis that allows the identification of modular transcriptional repertoires (communities) and the interactions between all the system's constituents through community detection. Changes in the degree of connections observed for hierarchically important hubs/genes in CT and DS networks corresponded to community changes. Distinct communities of highly interconnected genes were topologically identified in these networks. The role of miRNAs in modulating the expression of highly connected genes in CT and DS was revealed through miRNA-target analysis. Trisomy 21 gene dysregulation in thymus may be depicted as the breakdown and altered reorganization of transcriptional modules. Leading networks acting in normal or disease states were identified. CT networks would depict the "canonical" way of thymus functioning. Conversely, DS networks represent a "non-canonical" way, i.e., thymic tissue adaptation under trisomy 21 genomic dysregulation. This adaptation is probably driven by epigenetic mechanisms acting at chromatin level and through the miRNA control of transcriptional programs involving the networks' high-hierarchy genes.

| S-EPMC4884935 | biostudies-literature

Modular transcriptional repertoire analyses identify neutrophil signature as candidate biomarker for lupus nephritis

Project description:Gene expression profiling (compared to healthy controls) to identify a biomarker for lupus nephritis

2022-01-02 | GSE72326 | GEO

Modular transcriptional repertoire analyses of adults with systemic lupus erythematosus reveal distinct type I and type II interferon signatures.

Project description:The role of interferon-? (IFN?) in the pathogenesis of systemic lupus erythematosus (SLE) is strongly supported by gene expression studies. The aim of this study was to improve characterization of the blood IFN signature in adult SLE patients.Consecutive patients were enrolled and followed up prospectively. Microarray data were generated using Illumina BeadChips. A modular transcriptional repertoire was used as a framework for the analysis.Our repertoire of 260 modules, which consisted of coclustered gene sets, included 3 IFN-annotated modules (M1.2, M3.4, and M5.12) that were strongly up-regulated in SLE patients. A modular IFN signature was observed in 54 of 62 patients (87%) or 131 of all 157 samples (83%). The IFN signature was more complex than expected, with each module displaying a distinct activation threshold (M1.2 < M3.4 < M5.12), thus providing a modular score by which to stratify SLE patients based on the presence of 0, 1, 2, or 3 active IFN modules. A similar gradient in modular IFN signature was observed within patients with clinically quiescent disease, for whom moderate/strong modular scores (2 or 3 active IFN modules) were associated with higher anti-double-stranded DNA titers and lower lymphocyte counts than those in patients with absent/mild modular scores (0 or 1 active IFN modules). Longitudinal analyses revealed both stable (M1.2) and variable (M3.4 and M5.12) components of modular IFN signature over time in single patients. Interestingly, mining of other data sets suggested that M3.4 and M5.12 could also be driven by IFN? and IFN?.Modular repertoire analysis reveals complex IFN signatures in SLE, which are not restricted to the previous IFN? signature, but which also involve IFN? and IFN?.

| S-EPMC4157826 | biostudies-literature

Modular Transcriptional Repertoire and microRNA-target Analyses in Thymic Tissue of Down Syndrome Infants

Project description:Trisomy 21- driven transcriptional alterations in human thymus were characterized through gene coexpression network (GCN) and microRNA-target analyses. We used whole thymic tissue (corticomedullar sections) - obtained at heart surgery from Down syndrome (DS) and karyotipically normal individuals (CT) - and a network-based approach for GCN analysis that allows the identification of modular transcriptional repertoires and the interactions between all the system’s constituents through community detection. Changes in the degree of connections observed for hierarchically important hubs/genes in CT and DS gene networks corresponded to sub-network changes, i.e. module (communities) changes. Distinct communities of highly interconnected gene sets were topologically identified for DS and CT networks. The role of microRNAs in modulating the expression of highly connected genes in CT and DS was revealed through microRNA-target analysis. Trisomy 21 gene dysregulation in thymus may well be depicted as the breakdown and altered reorganization of functional modules.

2017-02-09 | GSE69210 | GEO

Systems Immunology Analyses Following Porcine Respiratory and Reproductive Syndrome Virus Infection and Vaccination.

Project description:This study was initiated to better understand the nature of innate immune responses and the relatively weak and delayed immune response against porcine reproductive and respiratory syndrome virus (PRRSV). Following modified live virus (MLV) vaccination or infection with two PRRSV-2 strains, we analyzed the transcriptome of peripheral blood mononuclear cells collected before and at three and seven days after vaccination or infection. We used blood transcriptional modules (BTMs)-based gene set enrichment analyses. BTMs related to innate immune processes were upregulated by PRRSV-2 strains but downregulated by MLV. In contrast, BTMs related to adaptive immune responses, in particular T cells and cell cycle, were downregulated by PRRSV-2 but upregulated by MLV. In addition, we found differences between the PRRSV strains. Only the more virulent strain induced a strong platelet activation, dendritic cell activation, interferon type I and plasma cell responses. We also calculated the correlations of BTM with the neutralizing antibody and the T-cell responses. Early downregulation (day 0-3) of dendritic cell and B-cell BTM correlated to both CD4 and CD8 T-cell responses. Furthermore, a late (day 3-7) upregulation of interferon type I modules strongly correlated to helper and regulatory T-cell responses, while inflammatory BTM upregulation correlated more to CD8 T-cell responses. BTM related to T cells had positive correlations at three days but negative associations at seven days post-infection. Taken together, this work contributes to resolve the complexity of the innate and adaptive immune responses against PRRSV and indicates a fundamentally different immune response to the less immunogenic MLV compared to field strains which induced robust adaptive immune responses. The identified correlates of T-cell responses will facilitate a rational approach to improve the immunogenicity of MLV.

| S-EPMC8716554 | biostudies-literature

Modular repertoire analyses identify dynamic type I and type II interferon transcriptional signatures in adult SLE patients

Project description:Gene expression profiling (compared to healthy controls) to identify patients with active SLE disease and patients with quiescent disease 157 “SLE” and 20 “Healthy controls of SLE were followed up for up to 3 years. Clinical assessment, current treatment, laboratory results and SLEDAI score were collected at each visit (V1, V2...). SLE patients are compared to control groups.

2014-04-01 | E-GEOD-49454 | biostudies-arrayexpress

Modular Transcriptional Repertoire and microRNA target Analyses Characterize Genomic Dysregulation in the Thymus of Down Syndrome Infants

2017-02-09 | GSE70573 | GEO

Modular repertoire analyses identify dynamic type I and type II interferon transcriptional signatures in adult SLE patients

Project description:Gene expression profiling (compared to healthy controls) to identify patients with active SLE disease and patients with quiescent disease

2014-04-01 | GSE49454 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data