Figure 2

Comparative ontological characterisation of the time-dependent spinal cord gene expression profiles obtained from animal models of spinal cord compression and G93A SOD1 mutant rats using Bead array technology (Illumina) and High-Throughput GoMiner. The heat chart reports the main functional headings containing clusters of parent-child and functionally related Gene ontology (GO) categories (total output from High-Throughput GoMiner: 232 GO categories) obtained from the 9 subsets of differentially expressed genes. The 9 subsets of differentially regulated genes have been obtained comparing thoracic cord at 30 minutes, 4 hours, 24 hours and 7 days after compression injury and at 30 minutes and 4 hours after laminectomy with healthy 10-weeks old spinal cord, and comparing the G93A SOD1 mutant spinal cord from animals at a pre-symptomatic stage, at onset and at end-stage disease with spinal cord from wild-type littermates at pre-symptomatic, onset and end-stage disease time-points. GO categories are computed from the 9 text files containing the changed genes by High-Throughput GoMiner, according to estimations of significance by false discovery rate (FDR, cut off <0.05). The functional headings contain GO categories identified as significantly up-regulated predominantly in the spinal cord compression molecular profiles (A), in both G93A SOD1 mutant and injured spinal cord (B), and only in the spinal cord from the G93A SOD1 mutant animals (C). Functional headings down-regulated in spinal cord from both experimental conditions are also reported (D). The degree of differential regulation of each functional heading is expressed at a specific time point as the average of the false discovery rates (aFDR) of all the functional heading's GO categories at this specific time-point and represented in the heat-chart with a colour code, in which lighter colours represent a higher level of differential regulation and the darker ones a lower level of differential regulation. "Differentially regulated": number of genes differentially regulated found in spinal cord gene expression analysis at each time point in the two experimental coditions. Sham*: 30 minutes after sham operation. Sham**: 4 hours after sham operation. GO***: number of GO categories in each functional heading. ****: transport of ions, neurotransmitters, potassium, calcium. *****: striated muscle, sarcomere, myosin, thick filaments.