A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations
Figure 5
Invasive colon cancer network predictions.
(A) Expression changes of selected E-genes following targeted S-gene knock-downs in HT29 colon cancer cells. Gene expression was measured in HT29 cells treated with a shRNA specifically targeting an S-gene (column of the matrix) relative to cells treated with a scrambled control shRNA (Irby et al., 2005). Colors indicate putatively inhibited E-genes (rows of the matrix) with up-regulated levels relative to control (red), activated E-genes with down-regulated levels relative to control (green), and unaffected E-genes with expression levels not significantly different from control (black). Biological replicates were available for KRT20, TFDP1, and GLS knock-downs. Genes were sorted by their attachment point and then by their LAR scores. (B) Cancer invasion network predicted by FG-NEM. For each pair of S-genes, the most likely interaction mode is shown. The same conventions used for illustrating interactions predicted for the yeast networks were used here. Some interactions were found to be significant at the 0.05 level (*) or 0.01 level (**) using a permutation test (see Methods). KRT20 and RPL32 were predicted to be equivalent and are therefore grouped together in a dashed oval. (C) Matrigel invasion assay in HT29 colon cancer cells. Genes predicted to be significantly attached to the network, CAPN12 and expressed sequence tag AA099748, resulted in a loss of the invasiveness phenotype when knocked-down by RNA interference. Genes not significantly attached to the network, MYO1G, BMPR1A, and COLEC12, did not result in significant loss of the invasive phenotype. A scrambled non-sense sequence also served as a negative control and did not result in a loss of HT29 cell invasiveness. Gene knock-downs in HT29 cells were validated by quantitative real time RT-PCR where mRNA levels of targeted genes were decreased by 70–80% compared to scrambled control shRNA-treated cells (data not shown). Data shown are the mean±S.E. of five independent experiments performed in quadruplicate. *Significantly different from scrambled control shRNA-treated cells (P<0.05) by ANOVA and post hoc Tukey test.