Naegle Lab Open Source Software


The ProteomeScoutAPI [publication] is a Python automatic programming interface for the ProteomeScout database downloads that allows for the easy interaction with post-translational modification information including proteins and their annotations. We used the database and API to test the hypothesis that mutations near sites of modifications are more likely to be involved in human disease (since they are more likely to affect the regulation and recognition of the modification). The results can be found in our iPythonNotebooks from the publication.

The motivation and features of the combined ProteomeScout and API are:

  • Enable the easy analysis of the PTMome
  • Allow for reproducible analyses
  • Allow for easy re-analysis in the future for the new PTMome

ProteomeScout is a database of post-translational modifications and their quantitative experiments.

Our Research Areas

  • Databases and resources for proteome-level PTM information

    A foundation of our work is the ability to have proteome information at our fingertips. This includes the current knowledge of tyrosine phosphorylation, quantitative measurements measured on those sites, and related protein annotations.  In enabling this research for our own lab, we also construct tools that can be used by the broader research community, with a focus on extendibility and reproducibility.

  • Inferring biological insight from high-dimensional data

    Kristen Naegle developed ensemble approaches to clustering of biological data in her Ph.D. work that demonstrated that one can infer function of tyrosine phosphorylation from quantitative measurements of the dynamic changes of network phosphorylation in cells in response to growth factor stimulation.  During her post-doctoral work, Dr. Naegle went on to show that robustness in clustering was predictive of protein interactions and inferred novel interactions in the epidermal growth factor receptor network.

  • SH2 domain binding

    A major piece of ongoing work in the lab is to develop methods that will allow us to identify what phosphotyrosines will be recognized by a binding domain. Specifically, we hope to push this area of research into arenas that allow us to predict the relative competition between domains for phosphotyrosine sequences and phosphotyrosine sequences for domains. This information will enable us to begin to predict the consequence of context differences between cells in response to the same extracellular cue. We will feel we have succeeded when these predictions can be used to explain complex network phenomena.

  • Engineering enzymatic interactions

    A major barrier to the study of protein phosphorylation is the ability to create phosphorylated proteins for in vitro study. The Naegle lab has been developing a cheap and fast method for producing phosphorylated proteins that capitalizes on observations made of enzymatic specificity.