DOI: 10.5061/dryad.dfn2z35bh
title: Custom made python script using network assignment and scoring to estimate the impact of biological processes.

description: Blood-borne factors are essential to maintain neuronal synaptic plasticity
 and cognitive resilience throughout life. One such factor is osteocalcin
 (OCN), a pro-youthful hormone produced by bones, that influences
 hippocampal neuronal homeostasis. However, the way how this blood-borne
 factor communicates with neurons remains unclear. Here, we show the
 importance of a core primary cilium (PC)-protein/autophagy axis in
 mediating OCN's effects. We found that OCN’s receptor, GPR158, is
 present at the PC of hippocampal neurons and mediates the regulation of
 autophagy machinery by OCN. During aging, autophagy and PC-core proteins
 are reduced in neurons and restoring their levels is sufficient to improve
 cognitive impairments in aged mice. Mechanistically, the induction of this
 axis by OCN is dependent on the PC-dependent cAMP response element-binding
 protein signaling pathway. Altogether, this study demonstrates that
 PC/autophagy axis is a gateway to mediate blood-borne factor-neuron
 communication and advances our understanding of the mechanism involved in
 age-related cognitive decline.
description: A custom made python script using network assignment and scoring
 to estimate the impact of biological processes and pathways in the context
 of specific functions. The code uses specific biological pathways by
 enriching them with gene ontologies (KEGG database, Reactome, etc.) and
 assigning them to nodes and connections, to determine centrality and
 peripherality of the factors
description: # NATAGING-Code
 [https://doi.org/10.5061/dryad.dfn2z35bh](https://doi.org/10.5061/dryad.dfn2z35bh) ## Description of the data and file structure Protein Group (Column A): A group of proteins that cannot be unambiguously identified as individual proteins based on the identified peptides. This occurs when multiple proteins share a significant number of peptides, making it difficult to determine which specific protein(s) are present. Protein IDs (Column B): Unique identifiers assigned to each protein in a database. These IDs are used to reference specific proteins and their associated information. Protein Names (Column C): The common names or systematic names assigned to proteins. These names are often derived from their function, structure, or the gene that encodes them. Genes (Column D): The mapped DNA that are known to encode the proteins in column “Protein Names”. A single gene can encode multiple protein isoforms through alternative splicing. First Protein Description (Column E): A brief description of the first protein in a protein group. This description may provide information about the protein's function, localization, or other relevant characteristics. **Vehicle: Experimental control group** Vehicle 1 (Column F): hippocampus mouse 1 treated with vehicle Vehicle 2 (Column G): hippocampus mouse 2 treated with vehicle Vehicle 3 (Column H): hippocampus mouse 3 treated with vehicle Vehicle 4 (Column I): hippocampus mouse 4 treated with vehicle Vehicle 5 (Column J): hippocampus mouse 5 treated with vehicle Vehicle 6 (Column K): hippocampus mouse 6 treated with vehicle   **OCN: Experimental osteocalcin group** OCN 1 (Column L): hippocampus mouse 1 treated with OCN OCN 2 (Column M): hippocampus mouse 2 treated with OCN OCN 3 (Column N): hippocampus mouse 3 treated with OCN OCN 4 (Column O): hippocampus mouse 4 treated with OCN OCN 5 (Column P): hippocampus mouse 5 treated with OCN OCN 6 (Column Q): hippocampus mouse 6 treated with OCN In columns F to Q, numbers represent fluorescent intensity values and have no unit NA cells in the table mean non available fluorescent intensity ### Files and variables Dataset available at PRIDE under the accession number 1-20241015-110055-3467911. ## Code/software home made python code ## Access information Other publicly accessible locations of the data: * KEGG Data was derived from the following sources: * KEGG * PRIDE under the accession number 1-20241015-110055-3467911