Aligning Cross-Species Interactomes for Studying Complex and Chronic Diseases
Neurodegenerative diseases (NDs) are a group of complex disorders characterized by the progressive degeneration and dysfunction of neurons in the central nervous system. NDs encompass many conditions, including Alzheimer’s disease and Parkinson’s disease. Alzheimer’s disease (AD) is a complex diseas...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-07-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/13/7/1520 |
| _version_ | 1827732598513729536 |
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| author | Marianna Milano Pietro Cinaglia Pietro Hiram Guzzi Mario Cannataro |
| author_facet | Marianna Milano Pietro Cinaglia Pietro Hiram Guzzi Mario Cannataro |
| author_sort | Marianna Milano |
| collection | DOAJ |
| description | Neurodegenerative diseases (NDs) are a group of complex disorders characterized by the progressive degeneration and dysfunction of neurons in the central nervous system. NDs encompass many conditions, including Alzheimer’s disease and Parkinson’s disease. Alzheimer’s disease (AD) is a complex disease affecting almost forty million people worldwide. AD is characterized by a progressive decline of cognitive functions related to the loss of connections between nerve cells caused by the prevalence of extracellular <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mi>A</mi><mi>β</mi></mrow></semantics></math></inline-formula> plaques and intracellular neurofibrillary tangles plaques. Parkinson’s disease (PD) is a neurodegenerative disorder that primarily affects the movement of an individual. The exact cause of Parkinson’s disease is not fully understood, but it is believed to involve a combination of genetic and environmental factors. Some cases of PD are linked to mutations in the LRRK2, PARKIN and other genes, which are associated with familial forms of the disease. Different research studies have applied the Protein Protein Interaction (PPI) networks to understand different aspects of disease progression. For instance, Caenorhabditis elegans is widely used as a model organism for the study of AD due to roughly 38% of its genes having a <i>human</i> ortholog. This study’s goal consists of comparing PPI network of <i>C. elegans</i> and <i>human</i> by applying computational techniques, widely used for the analysis of PPI networks between species, such as Local Network Alignment (LNA). For this aim, we used L-HetNetAligner algorithm to build a local alignment among two PPI networks, i.e., <i>C. elegans</i> and <i>human</i> PPI networks associated with AD and PD built-in silicon. The results show that L-HetNetAligner can find local alignments representing functionally related subregions. In conclusion, since local alignment enables the extraction of functionally related modules, the method can be used to study complex disease progression. |
| first_indexed | 2024-03-11T00:53:25Z |
| format | Article |
| id | doaj.art-059909797e194ba5a61cabfe5b27d82a |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-11T00:53:25Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-059909797e194ba5a61cabfe5b27d82a2023-11-18T20:09:38ZengMDPI AGLife2075-17292023-07-01137152010.3390/life13071520Aligning Cross-Species Interactomes for Studying Complex and Chronic DiseasesMarianna Milano0Pietro Cinaglia1Pietro Hiram Guzzi2Mario Cannataro3Department of Experimental and Clinical Medicine, University Magna Græcia, 88100 Catanzaro, ItalyData Analytics Research Center, University Magna Græcia, 88100 Catanzaro, ItalyData Analytics Research Center, University Magna Græcia, 88100 Catanzaro, ItalyData Analytics Research Center, University Magna Græcia, 88100 Catanzaro, ItalyNeurodegenerative diseases (NDs) are a group of complex disorders characterized by the progressive degeneration and dysfunction of neurons in the central nervous system. NDs encompass many conditions, including Alzheimer’s disease and Parkinson’s disease. Alzheimer’s disease (AD) is a complex disease affecting almost forty million people worldwide. AD is characterized by a progressive decline of cognitive functions related to the loss of connections between nerve cells caused by the prevalence of extracellular <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mi>A</mi><mi>β</mi></mrow></semantics></math></inline-formula> plaques and intracellular neurofibrillary tangles plaques. Parkinson’s disease (PD) is a neurodegenerative disorder that primarily affects the movement of an individual. The exact cause of Parkinson’s disease is not fully understood, but it is believed to involve a combination of genetic and environmental factors. Some cases of PD are linked to mutations in the LRRK2, PARKIN and other genes, which are associated with familial forms of the disease. Different research studies have applied the Protein Protein Interaction (PPI) networks to understand different aspects of disease progression. For instance, Caenorhabditis elegans is widely used as a model organism for the study of AD due to roughly 38% of its genes having a <i>human</i> ortholog. This study’s goal consists of comparing PPI network of <i>C. elegans</i> and <i>human</i> by applying computational techniques, widely used for the analysis of PPI networks between species, such as Local Network Alignment (LNA). For this aim, we used L-HetNetAligner algorithm to build a local alignment among two PPI networks, i.e., <i>C. elegans</i> and <i>human</i> PPI networks associated with AD and PD built-in silicon. The results show that L-HetNetAligner can find local alignments representing functionally related subregions. In conclusion, since local alignment enables the extraction of functionally related modules, the method can be used to study complex disease progression.https://www.mdpi.com/2075-1729/13/7/1520Alzheimer’s diseaseParkinson’s diseasePPI networknetwork alignmentlocal network alignment |
| spellingShingle | Marianna Milano Pietro Cinaglia Pietro Hiram Guzzi Mario Cannataro Aligning Cross-Species Interactomes for Studying Complex and Chronic Diseases Life Alzheimer’s disease Parkinson’s disease PPI network network alignment local network alignment |
| title | Aligning Cross-Species Interactomes for Studying Complex and Chronic Diseases |
| title_full | Aligning Cross-Species Interactomes for Studying Complex and Chronic Diseases |
| title_fullStr | Aligning Cross-Species Interactomes for Studying Complex and Chronic Diseases |
| title_full_unstemmed | Aligning Cross-Species Interactomes for Studying Complex and Chronic Diseases |
| title_short | Aligning Cross-Species Interactomes for Studying Complex and Chronic Diseases |
| title_sort | aligning cross species interactomes for studying complex and chronic diseases |
| topic | Alzheimer’s disease Parkinson’s disease PPI network network alignment local network alignment |
| url | https://www.mdpi.com/2075-1729/13/7/1520 |
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