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Interactions in multi-layer biological networks
Student:
Kate Petrenko
Supervisor:
Yury Barbioff, Institute of Bioinformatics Research & Education (IBRE)
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Introduction
Biological systems are often represented as networks: networks of protein-protein interactions, genetic interactions, or other types of molecular interactions. Although single-layer networks are widely used and studied in computational biology, few studies have attempted to systematically map and compare multiple network layers in different species. However, such analyses can provide interesting insights into the complexity of biological systems and their role in evolution.
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Aim and objectives of the project
Aim: explore correspondence between interactions in different biological networks (PPI, GI, CX)* for yeast and human. Find common patterns between organisms
Objectives:
*PPI - protein-protein interactions, GI - gene interactions, CX - co-expression data
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Databases
First step:
Second step:
All networks from GeneMANIA
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Results
The results of the intersection of the three networks in the vienna diagrams
H. sapiens
S. cerevisiae
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Results
The common interactions included genes that, on average, have slightly more interactions in different networks
H. sapiens
S. cerevisiae
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Results
Modularity metrics were calculated. The values indicate high modularity of the obtained networks
H. sapiens
S. cerevisiae
The figures show networks of genes with common interactions in all 3 networks
Modularity score:
0.86
Modularity score:
0.73
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Results
Yeast gene enrichment analysis reveals translation processes, chromosome organization, and other processes related to complex intermolecular structures
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Results
Human gene enrichment analysis reveals translation processes, energy metabolism, and other processes related to complex intermolecular structures
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Results
Next, we used a database GeneMANIA with more data, but the data were less homogeneous and genetic interactions were represented by more than screening studies.
S. cerevisiae
H. sapiens
6814
8 656
14 617
16 076
17 796
15 008
17 467
4 190
4 427
5 641
5 470
5 728
5 668
5 571
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Results
The modularity of these networks was lower, but the enrichment results were similar
| H. sapiens | S. cerevisiae |
Different databases | 0.73 | 0.86 |
GeneMANIA | 0.59 | 0.54 |
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Future plans
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