Proteomics and Systems Biology for Understanding Diabetic Nephropathy

Starkey, Jonathan M.; Tilton, Ronald G.

doi:10.1007/s12265-012-9372-9

Cited by 12 publications

(8 citation statements)

References 113 publications

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“…For example, the PCW for tenacin (uniprot ID: P24821) in a plasma based study of trauma was 8.6 × 10 −4 and a published estimate for the total protein concentration of plasma is 70 g/L, therefore the resulting concentration estimate for tenacin protein is 6.0 × 10 4 ng/ml [41–42]. Protein concentration by weight estimates can easily be converted to molarity estimates (nmol/ml) by dividing by the molecular weight of each protein.…”

Section: Absolute Expressionmentioning

confidence: 99%

MOPED Enables Discoveries through Consistently Processed Proteomics Data

Higdon

Stewart²,

Stanberry

et al. 2013

J. Proteome Res.

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The Model Organism Protein Expression Database (MOPED, http://moped.proteinspire.org), is an expanding proteomics resource to enable biological and biomedical discoveries. MOPED aggregates simple, standardized and consistently processed summaries of protein expression and metadata from proteomics (mass spectrometry) experiments from human and model organisms (mouse, worm and yeast). The latest version of MOPED adds new estimates of protein abundance and concentration, as well as relative (differential) expression data. MOPED provides a new updated query interface that allows users to explore information by organism, tissue, localization, condition, experiment, or keyword. MOPED supports the Human Proteome Project’s efforts to generate chromosome and diseases specific proteomes by providing links from proteins to chromosome and disease information, as well as many complementary resources. MOPED supports a new omics metadata checklist in order to harmonize data integration, analysis and use. MOPED’s development is driven by the user community, which spans 90 countries guiding future development that will transform MOPED into a multi-omics resource. MOPED encourages users to submit data in a simple format. They can use the metadata a checklist generate a data publication for this submission. As a result, MOPED will provide even greater insights into complex biological processes and systems and enable deeper and more comprehensive biological and biomedical discoveries.

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Section: Absolute Expressionmentioning

confidence: 99%

MOPED Enables Discoveries through Consistently Processed Proteomics Data

Higdon

Stewart²,

Stanberry

et al. 2013

J. Proteome Res.

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“…Identification is inherently biased for more abundant proteins, and for certain characteristics that make some peptides technically more easily identifiable. Comparison of studies is complicated by use of different methods for protein capture and separation, types of mass spectrometer equipment, as well as lack of standardization of sample processing and analysis [11]. Despite the technical difficulties, several studies have yielded useful insights.…”

Section: Omics Approaches To Diabetic Kidney Diseasementioning

confidence: 99%

“…Several previous reviews are excellent resources for the specifics of the techniques used [11] [12] [13] [14] [15] [16] [17]. We focus on rationale of these “omics” approaches, and highlight pertinent examples of early progress integrating different layers within the genome-phenome continuum.…”

Section: Introductionmentioning

confidence: 99%

Integrative Biology of Diabetic Kidney Disease

Harder¹,

Hodgin²,

Kretzler³

2015

Kidney Dis

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Background: The leading cause of end-stage renal disease in the US is diabetic kidney disease (DKD). Despite significant efforts to improve outcomes in DKD, the impact on disease progression has been disappointing. This has prompted clinicians and researchers to search for alternative approaches to identify persons at risk, and to search for more effective therapies to halt progression of DKD. The identification of novel therapies is critically dependent on a more comprehensive understanding of the pathophysiology of DKD, specifically at the molecular level. A more expansive and exploratory view of DKD is needed to complement more traditional research approaches that have focused on single molecules. Summary: In recent years, sophisticated research methodologies have emerged within systems biology that should allow for a more comprehensive disease definition of DKD. Systems biology provides an interdisciplinary approach to describe complex interactions within biological systems, including how these interactions influence systems' functions and behaviors. Computational modeling of large, system-wide, quantitative data sets is used to generate molecular interaction pathways, such as metabolic and cell signaling networks. Key Messages: Importantly, the interpretation of data generated by systems biology tools requires integration with enhanced clinical research data and validation using model systems. Such an integrative biological approach has already generated novel insights into pathways and molecules involved in DKD. In this review, we highlight recent examples of how combining systems biology with traditional clinical and model research efforts results in an integrative biology approach that significantly adds to the understanding of the complex pathophysiology of DKD.

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“…By providing consistently processed expression data, MOPED becomes a platform for data exploration and can accelerate hypothesis generation. As a resource, MOPED can be used for data validation and exploration (Chen and Penning, 2014;Staneva et al, 2013;Starkey and Tilton, 2012;Williams et al, 2014). Whether starting from a protein or gene ID, an experimental condition, or just a hunch, MOPED offers a way to explore data, share knowledge and find answers.…”

Section: Moped Data Interfacementioning

confidence: 99%

MOPED 2.5—An Integrated Multi-Omics Resource: Multi-Omics Profiling Expression Database Now Includes Transcriptomics Data

Montague¹,

Stanberry²,

Higdon³

et al. 2014

OMICS: A Journal of Integrative Biology

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Multi-omics data-driven scientific discovery crucially rests on high-throughput technologies and data sharing. Currently, data are scattered across single omics repositories, stored in varying raw and processed formats, and are often accompanied by limited or no metadata. The Multi-Omics Profiling Expression Database (MOPED, http://moped.proteinspire.org) version 2.5 is a freely accessible multi-omics expression database. Continual improvement and expansion of MOPED is driven by feedback from the Life Sciences Community. In order to meet the emergent need for an integrated multi-omics data resource, MOPED 2.5 now includes gene relative expression data in addition to protein absolute and relative expression data from over 250 large-scale experiments. To facilitate accurate integration of experiments and increase reproducibility, MOPED provides extensive metadata through the Data-Enabled Life Sciences Alliance (DELSA Global, http://delsaglobal.org) metadata checklist. MOPED 2.5 has greatly increased the number of proteomics absolute and relative expression records to over 500,000, in addition to adding more than four million transcriptomics relative expression records. MOPED has an intuitive user interface with tabs for querying different types of omics expression data and new tools for data visualization. Summary information including expression data, pathway mappings, and direct connection between proteins and genes can be viewed on Protein and Gene Details pages. These connections in MOPED provide a context for multi-omics expression data exploration. Researchers are encouraged to submit omics data which will be consistently processed into expression summaries. MOPED as a multi-omics data resource is a pivotal public database, interdisciplinary knowledge resource, and platform for multi-omics understanding.

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Proteomics and Systems Biology for Understanding Diabetic Nephropathy

Cited by 12 publications

References 113 publications

MOPED Enables Discoveries through Consistently Processed Proteomics Data

MOPED Enables Discoveries through Consistently Processed Proteomics Data

Integrative Biology of Diabetic Kidney Disease

MOPED 2.5—An Integrated Multi-Omics Resource: Multi-Omics Profiling Expression Database Now Includes Transcriptomics Data

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