Questions tagged [networks]

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How to calculate module-trait relationship when trait data is in binary format?

I have a dataset of 50 breast cancer samples. These samples are classified into four subtypes Lum A, Lum B, Her2 and Basal. I have been working with lncRNAs and protein-coding genes. To identify the ...
2
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0answers
87 views

Locate KEGG/Reactome pathways in user defined network

I am working on big networks of genes. I want to locate KEGG/Reactome pathways in my network. I have already tried cytoKegg and ReactomeFI (Plugins of Cytoscape), they only give me a list of Pathways ...
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0answers
33 views

Network analysis: confidence score (STRING database) validation

I am working on network analysis of differentially expressed genes, but the problem I am facing is that the gene set is very small (around 16 genes only), so when I'm trying to build an interaction ...
1
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0answers
10 views

How can I associate centrality score of genes(vertices) in a GRN with the probabilistic model in terms of cause and effect?

I'm learning to build Bayesian Network Based Modeling of Gene Regulatory Network of Cancerous Cellular Cells. So far, I have learned to form a Bayesian Network based on nature of genes(i.e Functional ...
1
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0answers
56 views

How to write the subclusters in file?

I have constructed a gene co-expression network from RNA-seq data. The network file is in edge list format of memory around 1gb which was created by calculating Pearson correlation of each gene pairs ...
1
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0answers
429 views

How to format the Nexus file to create geographical maps with haplotypes in PopArt?

I'm trying to create a map in PopArt that allows me to visualise the distribution of several species. These are my Traits (=species) and GeoTags blocks: ...
1
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0answers
56 views

The slopes of gene networks

I have a gene network that I clustered into 8 parts. I calculated the degree distribution of the clusters using Cytoscape and the slope of the clusters range from $0.7$ to about $1.3$. From ...
1
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0answers
298 views

Create gene network from list of genes

This has also been posted on biostars I had an initial bipartite transcriptional regulatory network for bees. My idea is to create a similar network for termites so as to check if similar genes are ...
1
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0answers
76 views

Help with generating network from gene expression data

I'm struggling to figure out how to go from gene expression data to be able to create a network out of the most expressed genes in a cell line. Ok, I have developed an application for Cytoscape where ...
0
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0answers
17 views

What are good resources to learn the basics of graph theory

I just spent half a day "debugging" a script that tried to get the betweenness centrality of a weighted graph with negative weights. However the package I used for that julia's ...
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0answers
17 views

How to analyze the correlation of two different tissue gene expression under three conditions?

I have three conditions A, B, and C. For each state, I have gene expression data of two different tissues(liver and pancreas). I am studying the possible network/correlation/ between tissues for each ...
0
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0answers
37 views

Regarding RNA seq data analysis and building coexpression network

I have some questions regarding RNA seq analysis if you can suggest anything it will help me a lot. I am currently normalizing RNA seq data for comparing genes expression within and between samples. ...
0
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0answers
32 views

Kinetics “Master Equation”

In stochastic (probabilistic) models, the evolution of a system over time is calculated using a "Master Equation" which also factors the external and internal noise / perturbations in order to more ...
0
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0answers
22 views

Comparing between different set of clusters produced from the same network

I have a set of eight gene clusters which I obtained from clustering a network. However, I had to update the genes in the network at a later stage which lead to certain deletions (genes not present in ...