Developing data products

Course project

Mihaly Varadi
Biotech engineering

Background

Proteins are molecular machines that allow living cells to function as tiny factories. These machines are built from blocks called amino acids. Messenger RNAs (mRNAs) are polynucleotides that encode the blueprints of the different proteins, storing the sequence of the building blocks.

The expression levels of mRNAs change during the lifetime of an organism, and it is our intention to follow such changes for specific proteins of interest.

In this case we are mostly focusing on flexible proteins, that lack stable structures. These are the so-called intrinsically disordered proteins.

Purpose of the applet

The conservation of a feature between different species can indicate the functional importance. Therefore, the Shiny applet presented here is creating interactive plots that can visualize the conservation of certain features across different related species in different subgroups of expression level changes. The features investigated are:

  1. The conservation of amino acid residues
  2. The conservation of intrinsic disorder

The full dataset is subsetted, using the slide bar into groups of certain expression change levels, and two interactive plots are generated:

  1. Hexbin plot, showing the binned sequence- and disorder conservation score pairs
  2. Density plot, showing the distribution of sequence- and disorder scores (compared to a reference)

Example density plot

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Example hexbin plot

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