Difference between revisions of "Modelling pathways crosstalks as closed walks and cycles on graphs"
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==Modelling pathways crosstalk in gene/protein networks as closed walks & cycles on graphs== | ==Modelling pathways crosstalk in gene/protein networks as closed walks & cycles on graphs== | ||
| − | + | ==Definitions== | |
Our project was to analyse and quantify interactions between different biological pathways. Those interactions are named closed walks. A closed walks is a sequence of interactions between genes that starts and ends at the same gene. A cycle is a closed walk that never goes twice through the same gene except for the gene from which the interactions start and end. A cross talk is a closed walk that goes through genes from two different pathways, meaning that those pathways communicate and regulate each other through their genes/proteins interactions. | Our project was to analyse and quantify interactions between different biological pathways. Those interactions are named closed walks. A closed walks is a sequence of interactions between genes that starts and ends at the same gene. A cycle is a closed walk that never goes twice through the same gene except for the gene from which the interactions start and end. A cross talk is a closed walk that goes through genes from two different pathways, meaning that those pathways communicate and regulate each other through their genes/proteins interactions. | ||
| − | + | ==Research questions== | |
We had 3 research questions: | We had 3 research questions: | ||
* Are some functional pathways more prone to crosstalk than the others? If so, which ones? | * Are some functional pathways more prone to crosstalk than the others? If so, which ones? | ||
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''the analysis concentrates on closed walks of length 2, 3 and 4 only, for computational power reasons.'' | ''the analysis concentrates on closed walks of length 2, 3 and 4 only, for computational power reasons.'' | ||
| − | =Methods= | + | ==Methods== |
To answer the research questions we were provided with data containing genes' names, for each gene was indicated the different biological pathways it played a role into (each gene is involved in many different pathways). We first selected three different pathways to analyse, so that we could compare the interactions between each pair of those pathways. The chosen pathways were: | To answer the research questions we were provided with data containing genes' names, for each gene was indicated the different biological pathways it played a role into (each gene is involved in many different pathways). We first selected three different pathways to analyse, so that we could compare the interactions between each pair of those pathways. The chosen pathways were: | ||
* Cell differentiation | * Cell differentiation | ||
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* Programmed cell death | * Programmed cell death | ||
| − | + | We also got a csv file containing | |
| − | We | ||
Revision as of 09:38, 4 June 2024
Contents
Modelling pathways crosstalk in gene/protein networks as closed walks & cycles on graphs
Definitions
Our project was to analyse and quantify interactions between different biological pathways. Those interactions are named closed walks. A closed walks is a sequence of interactions between genes that starts and ends at the same gene. A cycle is a closed walk that never goes twice through the same gene except for the gene from which the interactions start and end. A cross talk is a closed walk that goes through genes from two different pathways, meaning that those pathways communicate and regulate each other through their genes/proteins interactions.
Research questions
We had 3 research questions:
- Are some functional pathways more prone to crosstalk than the others? If so, which ones?
- What are the genes that are apparent “entry points” for the crosstalk with other pathways?
- Is crosstalk a symmetric process, i.e. do both pathways “need each other” the same, or is one rather “exploiting” the other for input stimuli?
the analysis concentrates on closed walks of length 2, 3 and 4 only, for computational power reasons.
Methods
To answer the research questions we were provided with data containing genes' names, for each gene was indicated the different biological pathways it played a role into (each gene is involved in many different pathways). We first selected three different pathways to analyse, so that we could compare the interactions between each pair of those pathways. The chosen pathways were:
- Cell differentiation
- Mitotic cell cycle
- Programmed cell death
We also got a csv file containing
