PMC

Venn diagram depicting the numbers of differentially expressed genes shared among the cytoplasm, polysomes, and whole cells (A), between polysomes and cytoplasm (B), and between polysomes and whole cells (C) from SMAD4^–/– versus SMAD4+ BxPC3 cells.

Venn diagrams depicting the numbers of differentially expressed genes between, among, and exclusively of the cytoplasm, polysomes, and whole cells from SMAD4^–/– versus SMAD4+ BxPC3 cells using the Agilent microarray platform (A) and the Illumina bead array platform (B).

Experimental design (A) and representative polysome profiles of SMAD4^–/– (Sham) BxPC3 cells (B), SMAD4+ BxPC3 cells (C), and polysomes from SMAD4^–/– BxPC3 cells treated with 100 μM EDTA for 10 min (D). [Color figure can be seen in the online version of this article, available at http://wileyonlinelibrary.com/journal/mc]

The numbers of differentially expressed genes (DEGs) between, among, and exclusively of the nucleus, cytoplasm, and polysomes from SMAD4^–/– versus SMAD4+ BxPC3 cells shown in a Venn diagram (A) and in the different cell compartments (B). The percentages in parentheses are the percent of shared DEGs for the two corresponding RNA populations.

The numbers of differentially expressed genes (DEGs) and corresponding pathways derived from Gene Ontology Biological Processes-FAT (BPs) in the different cell compartments between and exclusively of the nucleus, cytoplasm, and polysomes in SMAD4^–/– versus SMAD4+ BxPC3 cells. The percentages in parentheses are the percent of shared DEGs and shared BPs, respectively, for the two corresponding RNA populations.

Models depicting how differentially expressed polysome RNA populations may be distributed in the cell. A single RNA species is depicted in each model to be representative of a given polysome RNA population. Model 1 (A) represents the common RNAs differentially regulated between nucleus and polysomes but not cytoplasm (579/1091 = 53.1%). Model 2 (B) represents those RNAs regulated independently at the polysome level and are differentially expressed only in the polysomes but not nucleus and cytoplasm (485/1091 = 44.5%).

Network map of key signaling pathways associated with PDAC and encoded by differentially expressed mRNA from polysomes of SMAD4^−/− versus SMAD4+ BxPC3 cells. Pink shapes represent mRNAs expressed at relatively higher levels, those in green at relatively lower levels, and those in gray are not differentially expressed (P-value ≤0.05). Proteins and biological processes with blue halos represent a set of genes in a biological process that include genes expressed at both relatively higher and lower levels. Values in parentheses represent relative changes in RNA levels of greater than 1.2-fold. Fold changes less than 1.2-fold are represented with a + or − sign preceding the gene symbol. Hexagon, signaling protein; Rectangle, biological process; Diamond, ligand; Oval, small molecule; Boomerang, kinase; , receptor; , transcription factor. [Color figure can be seen in the online version of this article, available at http://wileyonlinelibrary.com/journal/mc]