We mapped gene expression data onto optimally arranged grid representations of pathways of the metabolic network and applied Haar wavelet transforms onto defined pathways of the network to combine gene expression values from neighboring enzymes.
We briefly summarize the two steps (for more details, see Schramm et al. [ 1]): Step 1 (preprocessing of pathway information): To run a PathWave analysis which involves the use of wavelet transforms (see below), compact 2D grid representations of pathways are required.
Here, we presented a considerably improved version that, among other changes, uses a novel LP formulation to optimally embed pathway networks into compact 2D lattice grids and provides a more flexible and user-friendly interface including ready-to-use pre-arranged 2D grid representations of pathway collections for now six organisms.
Here, we present the new, entirely revised and refined version of PathWave with several substantial improvements: i. a faster and more efficient arrangement of 2D grid representations of pathway networks (see below), ii.
Step 2 (analysis of expression data): To identify pathways that are differentially regulated between two conditions or subsets of gene expression data, PathWave first associates gene expression levels with metabolic reactions or signaling proteins, thus mapping the expression data of each individual sample onto the 2D lattice grids of the pathways (see Figure 1B).
For the 22 days of its existence, the balloon offered the possibility, in its randomness, of getting lost, of losing oneself, in contradistinction to the grid of precise, rectangular pathways under our feet.
Pershin and Di Ventra's scheme is to replicate an ordinary maze of vertical and horizontal pathways with a grid of many—hundreds or perhaps thousands interconnected memristors.
These optimal 2D grid representations need to be computed only once for a given set of pathways and can be saved for later use.
Last year they helped to safeguard 140,000 miles of pathways.
In the night our maze of pathways is audibly retraced.
