Questions tagged [network]

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Is there a measure for degree of reticulation in a phylogenetic network?

When working with phylogenetic networks, how does one talk about reticulate (i.e., web-like) the branches are? Is there a standard measure of this?
Namenlos's user avatar
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1 vote
1 answer
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Modularity score comparison between different algorithms in network analysis

I used different algorithms for splitting my large gene network into different sub-networks using Cytoscape. I compared the modularity scores and decided that the algorithm with the best modularity ...
The Last Word's user avatar
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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 ...
Jonathan's user avatar
1 vote
0 answers
47 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?
girl101's user avatar
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2 votes
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35 views

How does fungi network transfer substances between plants?

How does fungi network transfer substances between plants? I recently read a short article about fungi network. And I am wondering about how fungi network works (Mechanism). Plants have fungi ...
KYHSGeekCode's user avatar
2 votes
0 answers
76 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-...
uhoh's user avatar
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1 vote
0 answers
26 views

Gene networks in insects

I am working on gene networks and I currently have the honey bee gene network to work with. What I am missing is a gene network that I could compare it with. Could you please guide me to a database/...
The Last Word's user avatar
1 vote
0 answers
39 views

Get Network Out of proteins of interest

I have generated a list of Proteins using oncogeenes and suppressor genes of cancer. I have 5827 mapping identifier for 3916 interactions using STRINGdb R package . How do I build a network of 200k ...
A M's user avatar
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2 votes
0 answers
92 views

String-db locally downloaded

I need a ppi network of cancer and it should have 200k to 300k proteins (nodes) As the web inteface don't allow more than 2000 ...
A M's user avatar
  • 155
-1 votes
1 answer
186 views

Stringdb using R Bioconductor package

I need to retreive a large dataset from String-db. I 'm newbie in R so even with the documentation , I could not get the dataset fron String How do I do to retreive a network from String 2k to 3k ...
A M's user avatar
  • 155
2 votes
1 answer
274 views

R Stringdb bioconductor

I 'm using STRINGdb package from biconductor to manipulate String database of ppi I'm newbie and I don't find the documentation of the package useful for me . I wanna extract the associated network ...
A M's user avatar
  • 155
0 votes
1 answer
50 views

Retrieve the associated annotation from Uniprot

I have a dataset that I extracted using Cytoscape and STRINGAPI Hoz can I retreive the annotation of that network from uniprot as it has more than 1k proteins . and doing it manually is not possible
A M's user avatar
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Cytoscape export network

I'm using Cytoscape to visualise a ppi network having 2000 proteins ... I m trying to export it but the supported format are only cytoscype formats not a usable ones and for the table format the ...
A M's user avatar
  • 155
5 votes
1 answer
515 views

Best methodology to compare computed phylogeny tree with taxonomy?

I have computed a phylogenetic tree using an alignement of sequences, and I would like to : Compare it to the "known" taxonomy (uniprot/ncbi which I know is not the most up to date one) and extract a ...
Xqua's user avatar
  • 181
0 votes
2 answers
176 views

Does a gene that regulates itself necessarily be a transcription factor?

I am not a biologist, so please pardon the overly noob question. Some genes are transcription factors (TF) and regulate other genes. My question is: if a gene is NOT a TF gene, can it regulate itself? ...
TuanDT's user avatar
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1 answer
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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 ...
Train Heartnet's user avatar
0 votes
1 answer
217 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 ...
user96212's user avatar
2 votes
2 answers
292 views

Converting fmri data to association matrix

I am currently working on a new tool for the analysis of (large) weighted networks. Association matrices (correlation matrices) as obtained from fMRI data are perfect examples of the kind of data I am ...
M.B.'s user avatar
  • 203
5 votes
5 answers
468 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 ...
Jack Twain's user avatar
3 votes
1 answer
422 views

Biological meaning/interpretation of clustering coefficience

I have been looking for some time to find an answer to the following question. I would be grateful for any help/advice or directions. I work very frequently with large number of proteins and assess ...
Behzad Rowshanravan's user avatar
2 votes
0 answers
123 views

Predicting host-pathogen gene interaction networks

Background What we have are: ~20 genome sequences for a host species that come with gene annotations Several sequenced genomes for parasite/pathogens of these hosts Question What are the possible ...
hello_there_andy's user avatar
8 votes
1 answer
196 views

Could murder be modeled as an infectious disease?

Background "When swine flu hit the population it spiked in certain areas and tapered off in neighboring regions, it hits hardest where people have least protection and this pattern is more ...
hello_there_andy's user avatar
3 votes
2 answers
83 views

Have novel interactions or pathways been predicted by GRN or PPI data and later confirmed by experiment?

I've been learning about the gene regulatory network (GRN) and protein-protein interaction network (PPI) recently. I've found a huge amount of extremely interesting papers about how biological network ...
Matt Fenwick's user avatar
14 votes
3 answers
2k views

Databases for gene regulatory network graphs?

What databases are available for gene regulatory network graphs starting from a given gene? For example, starting from p53 gene, where can I find a gene regulatory network image that can be exported ...
yahoo301503's user avatar
5 votes
2 answers
234 views

How to typeset gene regulatory networks

I have a relatively simply gene regulatory network I would like to visualize, complete with the common arrow and bar symbols used to show, respectively, which genes enhance or repress with other genes....
Daniel Standage's user avatar