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Article title: An Experimentally supported model of the Bacillus subtilis global transcriptional regulatory network
Summary
This paper attempts to create a model of the transcriptional machinery within the Bacilius subtilis organism.
More specifically, the paper attempts to model the relationships between genes. When one gene is upregulated, how does that effect other genes?
GRN vs TRN vs GTRN
A gene regulatory network is any regulatory relationship between epigenetics factors within a cell. A transcriptional regulatory network within the context of this paper is a gene regulatory network that is inferred using transcriptional data.
Methods
Network component analysis
Network component analysis is a method with the same objective as PCA, namely to decompose a matrix X into 2 components P and A.
$$X = PA$$
However, PCA requires components to be orthogonal to each other. Network component analysis does not make any assumptions about the data.
Instead it requires a “prior network” \(P\) with known interactions between nodes. These interactions are quantified by values in the matrix \(P\).
The goal of network component analysis is to estimate the value of A.
Inferelator
The inferelator tool makes use of the baysian best-subset regression method for “inferring” the gene transcriptional network.
I’m thinking asking people to put a write up of their presentation on the wiki could be a good idea. That way, there could be a reference to the material while still allowing the presenter to put as little text on the slides as they want. I’m always split on whether or not to include detailed explanations in slides because that way they make better reference material, but usually the presentation itself is decreased in quality.