Figure 1.
IPA analysis of biological processes associated with expressed genes in the normal chondrocyte.
The classical IPA bar chart displays biological functions along the x-axis. The y-axis displays the - (log) significance. Functions are listed from most significant (higher bars) to least significant (lower bars) and the orange horizontal line denotes the threshold for significance (p-value of 0.05).
Figure 2.
Expression level of cartilage maturation stage specific marker genes in the normal chondrocyte.
Genes were classified according to their role in particular stages of cartilage maturation. Their Log2 intensity expression values are shown on the right, with high expression values (red), mid values (orange) and low values (blue). Expression values below 4 are considered as background (white). Most expressed genes belong to the proliferative group, suggesting that primary chondrocytes were mainly in a proliferative state.
Figure 3.
IPA analysis of biological processes associated with modulated genes in TDI chondrocytes.
Biological functions associated with significantly modulated genes are shown along the x axis of the bar graph and the - (log) significance along the y-axis. Functions are listed from most significant (higher bars) to least significant (lower bars). The threshold for significance (p-value of 0.05) is shown as an orange horizontal line.
Figure 4.
Normal v. TDI chondrocytes: modulated genes and cell cycle.
Modulated genes involved in different cell cycle processes are depicted as colored boxes along a diagram showing the five main stages (G1, S, G2, M and cytokinesis). Up-regulated genes are colored in red whereas down-regulated genes are colored in blue. Some key regulator genes, which are not modulated by FGFR3, are colored in grey.
Figure 5.
Normal v. TDI chondrocytes: modulated genes, ECM biosynthesis, cytoskeleton and adhesion.
Modulated genes are grouped according to their role in these different biological processes. Up-regulated genes are colored in red whereas down-regulated genes are colored in blue.
Figure 6.
Normal v. TDI chondrocytes: canonical pathways affected by mutated FGFR3.
Pathways are shown along the x axis of the classical IPA bar graph. The significance cutoff is shown as an orange horizontal line. Ratios (number of modulated gene present in a given pathway divided by the total number of genes that make up that pathway) are shown as orange points within the bar. Ratio values are shown on the right y axis.
Figure 7.
GO terms associated with up or down-regulated E2F targets.
Biological processes associated with either down-regulated or up-regulated E2F targets were assessed using FATIGO+. Significance of GO term abundance was computed against expressed genes. Terms in the table are grouped by GO term levels and are sorted by adjusted p-value. The normalized percentage of genes annotated to the functional term is given in the 1 vs #2 column.
Figure 8.
Relative expression levels are shown as a bar graph. Expression values were normalized to control in order to present expression ratios. Fold changes are given above each bar. Significant fold changes (5% cutoff) are indicated by an asterisk (*).
Figure 9.
Cytoplasmic localization and reduced staining for three transcription factors (SOX8, FOSL2, RUNX2) were observed in TDI chondrocytes (Y373C mutation). Staining for the intraflagellar transport protein (IFT74) is less marked in the mutant cells than the controls. Cytoplasmic staining for CHST3, a protein implicated in chondroitin sulfate biosynthesis, is less marked in TDI chondrocytes. Staining for ANGPT2 an NOGGIN in TDI chondrocytes is also less evident. Marked perinuclear staining of ID3 is observed in TDI chondrocytes. All the immunocytochemistry staining is in line with the fold change.