Proteomaps data download

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  1. Protein functional hierarchy
    The functional hierarchy is based on KEGG's functional hierarchy, but has been manually adapted. In the downloadable file, the same KEGG Orthology ID may still appear in several functional categories.

    Hierarchy tree | Hierarchy tree (levels 1-3) | Organism information | ID mapping files

  2. Abundance values for protein categories
    Abundance values for single proteins can be downloaded from the proteomaps home page. Here you can download abundance values for protein categories for a selection of data sets. In the files, protein abundances (possibly , weighted by protein chain lengths) are normalised by their total value. Sub-categories (first column) are marked by "-" (2nd level categories) and "--" (3rd level categories).

    Protein abundances | Protein abundances (length-weighted)

  3. Protein abundance ratios between functional categories
    Protein abundances are weighted by protein chain lengths.

    Abundance ratios | Abundance ratios (length-weighted)

  4. Protein abundance ratios (ranges obtained from permutation test)
    Instead of choosing, for each protein, the primary functional annotation, one of the possible annotations for this protein was chosen randomly. From 1000 such subsampled KEGG Orthology trees, we can estimate how different choices of the primary annotations would affect the weighted abundances of functional categories. The files contain, for each abundance value, the 10% quantile, the median, and the 90% quantile for a selection of data sets.

    Abundance quantiles | Abundance quantiles (length-weighted)

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Transcription Translation Folding, Sorting and Degradation DNA Maintenance Signal Transduction Vesicular Transport Cytoskeleton Cell Motility Cell Growth and Death Membrane Transport Central Carbon Metabolism Energy Metabolism Biosynthesis Other Enzymes Not Mapped