PANR (version 1.18.0)

data-Bakal2007: Rich morphological phenotypes for gene overexpression and RNA interference screens

Description

The data set we use here comes from quantitative morphological screening for 249 gene-overexpression or RNAi knock-down experiments. For each individual cell, 145 different geometric features were computed by imaging analysis, and are subsequently scored with NNs trained to discriminate seven reference TCs with distinctive morphologies. For each TC, NN z-scores were computed from all scored cells in this TC (more details in Bakal 2007).

Bakal2007: a matrix of NN z-scores with rows and columns corresponding to 249 TCs and seven reference TCs.

Bakal2007Cluster: unsupervised hierarchical clustering results by Bakal et al.

nodeColor: colors scaled according to the clustering results by Bakal et al.

bm1: an object of BetaMixture, which includes data and results for beta-mixture modelling on the association densities based on first-order cosine similarities of the phenotyping screens.

Usage

##see example for details

References

Bakal, C. and Aach, J. and Church, G. and Perrimon, N. (2007). Quantitative morphological signatures define local signaling networks regulating cell morphology. Science, 316(5832), 1753.

Examples

data(Bakal2007)
dim(Bakal2007)
data(bm)
bm1