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Mediators of Inflammation
Volume 2017, Article ID 7070469, 9 pages
https://doi.org/10.1155/2017/7070469
Research Article

Neuroinflammation and ALS: Transcriptomic Insights into Molecular Disease Mechanisms and Therapeutic Targets

Institute of Neurological Sciences, Italian National Research Council, Catania, Italy

Correspondence should be addressed to Sebastiano Cavallaro; ti.rnc@orallavac.onaitsabes

Received 20 March 2017; Revised 23 June 2017; Accepted 11 July 2017; Published 7 September 2017

Academic Editor: Thomas Möller

Copyright © 2017 Giovanna Morello et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Supplementary Figure 1. Alterations in the antigen processing and presentation pathway associated with SALS patients. This figure illustrates genes differentially expressed in SALS patients that are involved in the antigen processing and presentation process. Each encoded protein is labeled with two thermometers (1) or (2) that indicate expression levels in SALS cluster 1 and 2, respectively. Upward thermometers have red color and indicate up-regulated signals in SALS patients, down-ward (blue) ones indicate down-regulated signals. Colored hexagons on the vectors between objects describe the type of interaction where B = binding, C = cleavage, CM = covalent modification, Cn = competition, CS = complex subunit, GR = group relation, IE = influence on expression, P = phosphorylation, T = transformation, TR = transcriptional regulation, Tn = transport and CR indicates that an object belongs to a group of related proteins. Lines indicate activation (green), inhibition (red) or unspecified (grey) interactions between the molecules. The object shapes correspond to molecule type and are described in the Supplementary Figure 5. Supplementary Figure 2. Alterations in immune and inflammatory signaling observed in SALS patients. Genes involved in immune and inflammatory signaling that were differentially expressed in SALS patients versus controls were mapped on pathway. Thermometers labeled with (1) or (2) indicate expression levels in SALS cluster 1 and 2, respectively. Up-ward thermometers have red color and indicate up-regulated signals in SALS patients, down-ward (blue) ones indicate down-regulated signals. Colored hexagons on the vectors between objects describe the type of interaction where B = binding, C = cleavage, CM = covalent modification, Cn = competition, CS = complex subunit, GR = group relation, IE = influence on expression, P = phosphorylation, T = transformation, TR = transcriptional regulation, Tn = transport and CR indicates that an object belongs to a group of related proteins. Lines indicate activation (green), inhibition (red) or unspecified (grey) interactions between the molecules. The object shapes correspond to molecule type and are described in the Supplementary Figure 5. Supplementary Figure 3. Alterations in complement system signaling pathways (classical, lectin and alternative) observed in SALS patients. Thermometers labeled with (1) or (2) indicate expression levels in SALS cluster 1 and 2, respectively. Up-ward thermometers have red color and indicate up-regulated signals in SALS patients, down-ward (blue) ones indicate down-regulated signals. Colored hexagons on the vectors between objects describe the type of interaction where B = binding, C = cleavage, CM = covalent modification, Cn = competition, CS = complex subunit, GR = group relation, IE = influence on expression, P = phosphorylation, T = transformation, TR = transcriptional regulation, Tn = transport and CR indicates that an object belongs to a group of related proteins. Lines indicate activation (green), inhibition (red) or unspecified (grey) interactions between the molecules. The object shapes correspond to molecule type and are described in the Supplementary Figure 5. Supplementary Figure 4. Alterations in cytokine signaling observed in SALS patients. Thermometers labeled with (1) or (2) indicate expression levels in SALS cluster 1 and 2, respectively. Up-ward thermometers have red color and indicate up-regulated signals in SALS patients, down-ward (blue) ones indicate down-regulated signals. Colored hexagons on the vectors between objects describe the type of interaction where B = binding, C = cleavage, CM = covalent modification, Cn = competition, CS = complex subunit, GR = group relation, IE = influence on expression, P = phosphorylation, T = transformation, TR = transcriptional regulation, Tn = transport and CR indicates that an object belongs to a group of related proteins. Lines indicate activation (green), inhibition (red) or unspecified (grey) interactions between the molecules. The object shapes correspond to molecule type and are described in the Supplementary Figure 5. Supplementary Figure 5. Legend describing symbols used in MetaCore pathway. Supplementary Table 1. Pathway enrichment analysis on the entire list of statistically deregulated genes in SALS patients versus controls. Supplementary Table 2. Pathway enrichment analysis on the entire list of statistically deregulated genes in SALS1 and SALS2 patients compared to controls. Supplementary Table 3. Neuroinflammatory genes differentially expressed in SALS1. Supplementary Table 4. Neuroinflammatory genes differentially expressed in SALS2. Supplementary Table 5. Neuroinflammatory genes differentially expressed in SALS1 and SALS2. Supplementary Table 6. List of genes included in the SALS1-related PPI network. Supplementary Table 7. List of genes included in the SALS2-related PPI network. Supplementary Table 8. Pathway enrichment analyses on the list of statistically deregulated neuroinflammatory genes in SALS patients.

  1. Supplementary material