National Centers for Systems Biology

Data

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Center for Cell Decision Processes (MIT)

A compendium of signals and responses triggered by prodeath and prosurvival cytokines
Study of Transient Signaling Governing Cell Behavior
Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data

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Center for Genome Dynamics (The Jackson Laboratory)

Population Genetics
Linkage Disequilibrium
Gene Expression
Phenotype

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Center for Quantitative Biology (Princeton University)

All published data are made available on either our FTP site or within individual publications or their locally-hosted supplements. Published microarray data are also available within the Princeton University MicroArray database (PUMAdb). We provide separate FTP directories for large data collections, including:

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Center for Systems Biology (Institute for Systems Biology)

Data sharing outside the Center.  Data from Center-funded projects are deposited to public databases, posted on the Center website and/or made available by request, following publication.

Nucleic Acids:  Microarray data is deposited into ArrayExpress or the Gene Expression Omnibus database.  ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with MGED (Microarray Gene Expression Data) recommendations. The ArrayExpress data warehouse stores gene-indexed expression profiles from a curated subset of experiments in the repository.  As is the practice at the ISB, all data supporting Center research results and findings are made available upon publication, or public presentation, either through the Center website or as supplementary materials through publisher’s websites.

Proteomics:  All mass spectrometry data produced as part of the Center projects is deposited into the PeptideAtlas data repository and incorporated into PeptideAtlas ‘builds’.  The PeptideAtlas data repository is the largest public raw proteomics data repository containing over 100 large-scale experiments contributed from laboratories around the world.

During the tenure of the current Center: yeast protein interaction data has been deposited to the following public databases, as appropriate.

  • SGD (Saccharomyces Genome Database)
  • BIND (Biomolecular Interaction Network Database)
  • DIP (Database of Interacting Proteins)

Mammalian proteome sets have been deposited into:

  • MMPI (MIPS Mammalian Protein Protein Interaction database)
  • HPRD (Human Protein Reference Database)
  • IntAct (an open source resource for molecular interaction data)

Genotype and phenotype interaction data have been deposited into:

  • dbGaP (NCBI)
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Systems Biology Center New York (SBCNY)

Published data are made freely available for download on the following sections of the SBCNY website:

Interaction data is also deposited into PathwayCommons.

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