Biolayout express 3D

Unfiltered lists comprised of protein IDs with corresponding expression ratios at each time point relative to the equivalent timepoint wildtype value (available here: https://doi.org/10.7488/ds/2750 (2020)) were imported separately into BioLayout Express 3D and clustered based on relative expression profile in two separate comparisons—(a) 3 month Ppt1^−/− spinal cord vs. 7 month Ppt1^−/− spinal cord; and (b) or 3 month Ppt1^−/− spinal cord vs. 3 month Ppt1^−/− cortex. Algorithms in BioLayout Express 3D generate a visual network to represent each data set, in this study utilizing spatial proximity to represent the similarity in expression profile between nodes²⁵. It was therefore possible to isolate clusters of proteins grouped by similarity in terms of expression profiles over time. The resultant visual networks were utilized to distinguish expression clusters that followed trends in expression that favored either group or both groups (3 vs. 7 month spinal cord analysis—altered only at 3 months, altered only at 7 months and similar/progressive alterations; 3 month cortex vs. 3 month spinal cord analysis—differential detection only in cortex, differential detection only in spinal cord and similar alterations in both cortex and spinal cord at 3 months). These clusters were analyzed and input into Ingenuity Pathway Analysis (Ingenuity Systems).