Questions tagged [biological-networks]

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Is there a way for POPart to accept indels in chloroplastidial genes?

I need to construct a network concerning chloroplastidial genes using POPart. My problem is that POPart does not know how to deal with indels. I have already coded them using SeqState (simple indel ...
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network with all the interactions of the alpha-synuclein protein

I would like to make a network with all the interactions of the alpha-synuclein protein (in homo sapiens), that is, I would like to visualize the pathways where this protein participates, I would also ...
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What functions other than spore dispersal does a fruiting body serve in a mycelial network?

I'm not exactly sure if this is the appropriate forum to ask this, so apologies in advance. My question is both technical and general: what are the less obvious functions that the individual mushroom ...
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How to biologically interpret path weight summation in weighted and directed gene regulation network?

I've considered asking this question on Bioinformatics SE, Mathematics SE, and Stats SE, however I've judged that my question belongs on Biology SE because I am interested in a biological (domain-...
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Where are there analyzable signed directed network datasets?

I'm looking for biological datasets with specific properties that are available for me to analyze. Informally put, I have a hammer and I am looking for a nail. That is to say, I have an algorithm and ...
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Nutrition and experimental biology

We know that food in the stomach is present in the form of chyme treated with pepsin and hydrochloric acid, if we take food crush it with saliva and then treat it with Pepsin and HCl (in the lab),and ...
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May two reactions, that share the same reactant, fire at the same moment?

I'm studying metabolic networks from a bioinformatics point of view, but I guess my question is pretty biological so I thought that maybe here I could get the best answers. So, as the title says I ...
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Proteomics data Vs Transcriptomics data?

I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...
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How to integrate transcriptomics data with kinetic metabolic models?

I have created a convenience kinetics† model. Now, I want to integrate the transcriptomics data with my convenience kinetics model for altering/weighing the kinetic parameter values. I have ...
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131 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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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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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 ...
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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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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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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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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-...
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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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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 ...
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1answer
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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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911 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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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 ...
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82 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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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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380 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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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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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 ...
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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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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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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 ...