Toward effective sharing of high-dimensional immunology data

Snijder, Berend; Kandasamy, Richard K.; Superti‐Furga, Giulio

doi:10.1038/nbt.2974

Cited by 10 publications

(5 citation statements)

References 30 publications

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“…Specifically, glycerophospholipids (phosphatidylcholines [PC], phosphatidylethanolamines [PE], phosphatidylglycerols [PG], and phosphatidylserines [PS]) and sphingolipids (ceramides [Cer] and sphingomyelins [SM]) were quantified. The developing field of lipidomics still lacks standardized methods for data normalization, analysis, and visualization, as well as for lipid annotation ( Snijder et al., 2014 ). Here, lipid levels were normalized to total lipid content and transformed as log 2 fold-change relative to the sh:GFP control ( Figure S2 A).…”

Section: Resultsmentioning

confidence: 99%

A Conserved Circular Network of Coregulated Lipids Modulates Innate Immune Responses

Köberlin

Snijder

Heinz

et al. 2015

Cell

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SummaryLipid composition affects the biophysical properties of membranes that provide a platform for receptor-mediated cellular signaling. To study the regulatory role of membrane lipid composition, we combined genetic perturbations of sphingolipid metabolism with the quantification of diverse steps in Toll-like receptor (TLR) signaling and mass spectrometry-based lipidomics. Membrane lipid composition was broadly affected by these perturbations, revealing a circular network of coregulated sphingolipids and glycerophospholipids. This evolutionarily conserved network architecture simultaneously reflected membrane lipid metabolism, subcellular localization, and adaptation mechanisms. Integration of the diverse TLR-induced inflammatory phenotypes with changes in lipid abundance assigned distinct functional roles to individual lipid species organized across the network. This functional annotation accurately predicted the inflammatory response of cells derived from patients suffering from lipid storage disorders, based solely on their altered membrane lipid composition. The analytical strategy described here empowers the understanding of higher-level organization of membrane lipid function in diverse biological systems.

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Section: Resultsmentioning

confidence: 99%

A Conserved Circular Network of Coregulated Lipids Modulates Innate Immune Responses

Köberlin

Snijder

Heinz

et al. 2015

Cell

Self Cite

187

163

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“…Indeed, the concept of the rational filling of sparse zones of knowledge is starting to guide strategies in other collaborative efforts (Rolland et al, 2014;Snijder et al, 2014). Furthermore, we argue that the problem should be tackled systematically to capture the efficiencies that come with economies of scale and the learnings that derive from studying related proteins.…”

Section: Delving Into the ''Sparse Zones'' Of Our Knowledgementioning

confidence: 99%

A Call for Systematic Research on Solute Carriers

César-Razquin

Snijder

Frappier‐Brinton

et al. 2015

Cell

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503

480

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Solute carrier (SLC) membrane transport proteins control essential physiological functions, including nutrient uptake, ion transport, and waste removal. SLCs interact with several important drugs, and a quarter of the more than 400 SLC genes are associated with human diseases. Yet, compared to other gene families of similar stature, SLCs are relatively understudied. The time is right for a systematic attack on SLC structure, specificity, and function, taking into account kinship and expression, as well as the dependencies that arise from the common metabolic space.

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“…In general, complex datasets pose challenges to data discoverability, reproducibility, and reuse. Metadata documenting data provenance can play a crucial role in overcoming these challenges 4 . The ImmPort database architecture is designed to support and maintain a variety of multi-modal immunological data such as study method documentation, metadata and standardized data formats and terminologies.…”

Section: Introductionmentioning

confidence: 99%

ImmPort, toward repurposing of open access immunological assay data for translational and clinical research

et al. 2018

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Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data Analysis, and Resources—for data archiving, dissemination, analyses, and reuse. To date, more than 300 studies have been made freely available through the Shared Data portal (www.immport.org/immport-open), which allows research data to be repurposed to accelerate the translation of new insights into discoveries.

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Toward effective sharing of high-dimensional immunology data

Cited by 10 publications

References 30 publications

A Conserved Circular Network of Coregulated Lipids Modulates Innate Immune Responses

A Conserved Circular Network of Coregulated Lipids Modulates Innate Immune Responses

A Call for Systematic Research on Solute Carriers

ImmPort, toward repurposing of open access immunological assay data for translational and clinical research

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