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Questions tagged [biological-networks]

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0
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1answer
28 views

What does “count in gene set” mean?

I am trying to understand the analysis generated by STRING. In analysis for biological processes table, there is a column titled "count in gene set." This gives a value for example "68 of 498". What ...
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0answers
23 views

Where can I find datasets containing large phylogenetic networks?

There are many datasets out there for phylogenetic trees, one can example can be found here. However, I couldn't find something for phylogenetic networks. According to Wikipedia: A phylogenetic ...
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1answer
46 views

How does collaboration on reconstructing metabolic networks work?

I am a researcher in psychology and I am trying to come up with a framework/platform in which psychological phenomena can be studied from a dynamical systems / computational perspective in ...
3
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0answers
32 views

How to interpret the relationships of PTMs from BioGRID's data

On BioGRID Database, PTMREL is a file that describes relationships of the PTMs (Post Translation Modification) tabulated in a PTMTAB file. I have several issues with this file. Foremost, I am not ...
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0answers
41 views

Which gene regulatory network is the largest in human?

What is the maximum number of nodes involved in any gene regulatory network and which network is it, provided its from human?
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0answers
49 views

Biological significance of network parameters

I am currently working on networks and I have calculated various parameters for the network like diameter, average path length, average eccentricity, radiality etc. Could someone guide me to some ...
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0answers
36 views

Has network theory been successfully applied to protein expression within a cell?

I saw the following passage in the NPR 13.7 Cosmos & Culture commentary post The Big Idea Behind Big Data. Using the Internet's first generation of Big Data, researchers like physicist Albert-...
3
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1answer
153 views

Motifs in undirected networks

I have an undirected network and I am currently analyzing both three and 4 node motifs in the network. However, I can't find any articles which describe the biological significance of 3 of 4 node ...
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28 views

Gene networks for different tissues?

I currently work on gene networks and specifically, I analyze the brain gene regulatory network of an insect to understand its sexual behaviour. During a recent presentation, I got asked this question ...
5
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1answer
118 views

Explain a gene network to a first year undergrad

I have an adjacency matrix with list of genes connected to each other which signifies the gene network. How do you get this information that one gene is connected to other in the first place. Is it ...
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1answer
669 views

What's the difference between physical (direct) and functional (indirect) protein interaction?

I read that the Protein-Protein interactions one can consider are generally of two types, namely physical and functional, but I cannot get the difference between the two. I was just thinking that if ...
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0answers
40 views

Need to solve a “pseudo-metabolic” network for rates

following problem: I have data on a certain complex association network (from monomers 1 ... 8 to complexes of all combinations, such as, 12 ... 13 ... 18 and so on until 12345678, so that I know ...
0
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1answer
80 views

How are PPI networks constructed?

I am a CS graduate working in Computational Biology. While the theoretical aspects of both AP/MS (and the various types) and Y2h are quite clear to me, the actual technical aspect of building large-...
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1answer
429 views

What are some examples of undirected weighted networks in ecology?

I'm a math major with a current interest towards network theory. A network can be considered as a collection of nodes, and edges between these nodes signifying some relation between them. The most ...
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1answer
340 views

Applications of shortest path problem

The shortest path problem is the problem of finding the shortest path between multiple nodes. What are the applications of the shortest path problem in biology? A simple google search gives me this -...
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1answer
208 views

What pattern can be learned from the data of RNA seq counts and HiC matrix? [closed]

I now have some data on the RNA seq counts and related Hi-C matrix of gene segment on a chromosome. My concern is, basically, what can we do with these data so as to establish the connection between ...
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0answers
172 views

What software/approach to use to build a graph based on microarray gene expression correlation?

What software to use to build a graph based on microarray gene expression mutual correlation? I have tried Cytoscape`s Reactome FI and a recipe from R bioinformatics cookbook, however, need a more ...
0
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1answer
45 views

Biosphere that simulates sun and moon shifts

Is there an enclosed biosphere that artificially simulates the movement of the sun and moon at increased intervals? It is known that the sun and moon alter plant movements therefore I was wondering ...
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5answers
418 views

What are some examples of evolving networks in biology?

I'm a master student working on networks analysis in general. A network is something that has nodes and there are links between the nodes. Nodes and links could have attributes. An evolving network is ...
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2answers
308 views

Neuronal Architecture of the Brain

To what extent do brains (e.g. of humans) contain recurrent connections? I am studying artificial neuronal networks and frequently encountered the statement, that recurrent neural networks are ...