Questions tagged [networks]

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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?

I am working on using WGCNA for a bulk RNA-seq experiment. I have three experimental conditions (control, treatment 1, and treatment 2) and have a total sample size of 18 (6 per group). Using the ...
Meena Easwaran's user avatar
2 votes
1 answer
100 views

Coexpression network analysis

I have a question related with the most popular frameworks for network construction: WGCNA for weighted networks and igraph package for unweighted networks. What are the advantages or disadvantages of ...
María José's user avatar
0 votes
1 answer
132 views

How to find closely related genes for a specific gene from WGCNA modules?

I have used WGCNA by integrating several datasets which are processed in a similar way. Identified 17 modules, followed by performed pathway analysis with the genes present in those modules. Among all ...
user9114's user avatar
1 vote
0 answers
17 views

Running hubCheck utility from inside K8s's Pod

I'm trying to run hubCheck utility* from inside Kubernetes Pod but for some reason I get this Network error: ...
Bilal's user avatar
  • 111
0 votes
1 answer
273 views

Can you style network visualizations of directed graphs using NETWULF?

I want to draw directed graphs using networkx, followed by manual tuning of the visualization with the use of NETWOLF. Here is the example of a network. ...
Apppii092's user avatar
0 votes
1 answer
983 views

In Pygraphviz, How can I assign edge colors according to edge weights?

I am now drawing a weighted directed graph using Pygraphviz. The adjacency matrix A of the weighted directed graph is ...
Apppii092's user avatar
1 vote
0 answers
23 views

How to find disease association of disgenet with string db in homo sapiens

I want to work string-db to read the protein-protein interaction from it and I look up disease association from disgenet but the Ids do not seem to match-up and I do not know what to do. for example ...
nima moradi's user avatar
1 vote
0 answers
122 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 ...
Saransh Saxena's user avatar
1 vote
0 answers
19 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 ...
Mushahid Hussain's user avatar
0 votes
2 answers
643 views

STRINGdb: reverse map STRING identifiers to gene names?

Is there a functionality within STRINGdb package or in another environment to reverse map the STRING identifiers to Gene names? For example, the entire STRING network can be downloaded using the ...
Prradep's user avatar
  • 430
1 vote
1 answer
118 views

Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?

I am currently working on a network pharmacology project where I am supposed to find out the possible diseases our drug might have an effect on. I am not a bioinformatics student, so my knowledge in ...
Gee3's user avatar
  • 11
2 votes
1 answer
158 views

Metapath2vec on Drug-ADR Heterogeneous Graph

I am new in this field and I am having some problems regarding a new project. I built a graph using Drugbank Data connected to SIDER Adverse Reactions. I used Organ- level Terms to classify the ADRs ...
Cecilia's user avatar
  • 21
2 votes
1 answer
67 views

Populations genetics and dynamics of bacteria on a Graph

Disclaimer: I'm a physicist and I'm fairly new to Bioinformatics therefore somethings below may not make sense. My purpose: I would like to simulate genetic evolution of bacterial populations, ...
omega's user avatar
  • 123
4 votes
1 answer
412 views

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 ...
user9114's user avatar
1 vote
0 answers
62 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. ...
Citu's user avatar
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0 votes
1 answer
162 views

What's the difference between Barycenter Centrality and Closeness Centrality (Freeman)?

What's the difference between Barycenter Centrality and Closeness Centrality (Freeman)? Barycenter scores are calculated as 1 / (total distance from vertex v to all other vertices) in a strongly ...
黃家億's user avatar
  • 103
1 vote
1 answer
290 views

Importing a WGCNA co-expression network into a networkX graph in Python

Is there a way to generate a WGCNA co-expression graph in R, and then to import that graph into Python such that I can represent it using a networkX object?
An Ignorant Wanderer's user avatar
1 vote
1 answer
49 views

how to evaluate neural networks

I have made some architectures of neural networks in order to classify proteins in three categories. I have calculated true positive, true negative, false negative, false positive, Mathews, ...
marilu's user avatar
  • 101
2 votes
1 answer
189 views

Identifying mutually **exclusive** gene sets

I am interested in identifying gene pairs (or better: sets of genes) whose expression is mutually exclusive. Ideally, both genes (or gene sets) would be widely expressed but I am also interested in ...
Paul Brodersen's user avatar
0 votes
1 answer
2k views

WGCNA: Problem with selecting soft threshold

I have 25 tumor samples with counts data. Initially, I filtered out low expressed genes and then converted counts to varianceStabilizingTransformation using ...
beginner's user avatar
  • 631
1 vote
1 answer
54 views

Random networks in PPi

I am working with an in silico model to measure the distances between drugs targets and disease proteins of a disease. I would want to compare these distances with the distances of random networks but ...
PABLO GARCÍA ACERO's user avatar
-1 votes
1 answer
77 views

Module preservation and hub genes finding

I ran module preservation analysis between two condition and on the basis of preservation z summary i would to go for downstream analysis.So I m interested in looking for hub-genes of those modules ...
kcm's user avatar
  • 1,794
2 votes
1 answer
107 views

Visually summarizing phylogenetic networks

After having worked with Bayesian phylogenetic tree inference for some time, I am now trying out a method to infer network phylogenies. To get an idea of what it infers, I'd like to find a way of ...
Anaphory's user avatar
  • 121
0 votes
2 answers
242 views

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 ...
iamakhilverma's user avatar
1 vote
0 answers
59 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 ...
AISWARYA JAYAPRAKASH's user avatar
-1 votes
2 answers
344 views

How I debug this code?

I am trying to run CMSclassifier::classifyCMSfunction on my data but I am getting this error ...
Zizogolu's user avatar
  • 2,128
1 vote
1 answer
678 views

Clustering of gene co-expression network by igraph R package

I have constructed a gene co-expression network from RNA-seq data. The network has more than 10000 nodes and more than 1 million edges. The network file as an edge list format of memory around 1gb ...
AISWARYA JAYAPRAKASH's user avatar
0 votes
1 answer
292 views

How do I get the adjacency matrix from gene similarity network?

I am exploring application of Graph convolution network on gene similarity network. I am trying to explore genemania.org and https://string-db.org/ Please let me know where can I find the data for my ...
user avatar
1 vote
0 answers
40 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 ...
Osaama Shehzad's user avatar
4 votes
1 answer
110 views

Attractor Landscape Analysis

I have come across a modeling toolbox, ATLANTIS, which is able to determine cell fates in silico based on the input models provided. This MATLAB-based toolbox is built on a method called "Attractor ...
Osaama Shehzad's user avatar
1 vote
1 answer
48 views

Retrieving Metabolic networks from WIT Database

How can I get the dataset for all the 43 metabolic networks for this paper: https://www.nature.com/articles/35036627 It looks like the WIT database does not exist anymore.
ERSA's user avatar
  • 15
4 votes
3 answers
858 views

Error while loading a big file with Cytoscape

I installed Cytoscape 3.7.1 with java 1.8.0_191 in windows server 2012. I have a 7.4 GB csv file (about 1,500,000 reords) and when I tried to load it into the ...
user4219's user avatar
2 votes
2 answers
48 views

Visualize similar interactions in two homologous networks

Background I have two networks with homologous genes from two different species. To identify homologs I performed a functional comparison. One of the species is not well studied while the other one is ...
The Last Word's user avatar
0 votes
1 answer
67 views

How to create a graph of multi column gene dataset?

well, I'm new to Bio. what I'm going to do is create a network/graph of a dataset related to the genes I think. here's the sample of the nodes dataset with CSV format named lung-nodes : and this is ...
Mohammad Heydari's user avatar
1 vote
0 answers
49 views

What are fundamentals to work on bioinformatic data analysis ? [closed]

Well, I'm a MSc student in Information Technology Engineering, trying to become more familiar in the Complex networks specially Bioinformatic field to get more knowledge of cancer detection by ...
Mohammad Heydari's user avatar
4 votes
1 answer
116 views

Compare two networks of the same genes between two species

I had a set of genes for honey bees. I found the homologues of those genes in the house fly and created a network of the honey bee genes and a network of the homologous fly genes using STRING. I ...
The Last Word's user avatar
-1 votes
2 answers
37 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 ...
The Last Word's user avatar
0 votes
1 answer
179 views

How to calculate Gene Ontology terms in python

I am testing different Protein-Protein Interaction networks alignment tools. I observed that all alignment tools show some ...
Mani's user avatar
  • 109
0 votes
1 answer
34 views

Check if a set of genes fall more on a specific cluster than other clusters

I have a network which I clustered into 11 smaller clusters. I have a set of genes and I would like to check if statistically significant number of these genes fall on any specific cluster. One method ...
The Last Word's user avatar
1 vote
0 answers
1k 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: ...
LinuxBlanket's user avatar
0 votes
2 answers
284 views

Visualize network (graph) using "line" layout

I want to visualise a network in a way that the nodes are along a line (and the edges are not on that line). I have included a simple example below. Which network visualisation programs (Cytoscape, ...
Peter's user avatar
  • 2,634
7 votes
2 answers
183 views

Are gene names same across species?

I have a bunch of gene names of Apis mellifera (specifically 194). I used these gene names as an input on STRING database to create a network for Drosophila melanogaster. 54 of those genes were also ...
The Last Word's user avatar
2 votes
1 answer
229 views

Negative scale-free topology

I am trying to build gene co-expression networks with WGCNA by combining in-house and publicly available RNA-seq datasets. I am interested in identifying gene networks associated with different ...
lence's user avatar
  • 31
1 vote
0 answers
57 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 ...
The Last Word's user avatar
7 votes
1 answer
169 views

Network comparison of single cells (from sequencing data)

What methods can we use to compare networks (PPI, gene regulatory etc) created from single-cell gene expression (or proteomics) data? There are methods that construct networks by comparing two ...
Peter's user avatar
  • 2,634
1 vote
1 answer
159 views

Motif Discovery in Bipartite networks using Cytoscape

I am trying to find over-expressed motifs in a bipartite transcription factor gene network.My genes are not very well characterized, so finding functional motifs has been a challenge. I used the motif-...
The Last Word's user avatar
1 vote
0 answers
352 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 ...
The Last Word's user avatar
2 votes
1 answer
630 views

Program to make a haplotype network for a specific gene

Currently my lab manually uses pop art to make the network after using PHASE to id an individual's alleles. I would like to know how to generate the graph structure (i.e. the links between vertices), ...
Ryan Fahy's user avatar
3 votes
1 answer
54 views

How to read gene regulatory network edge list files?

The following is an excerpt from an edge list file from the Gene Regulatory Database, YeastNet v3 ...
Kunal24's user avatar
  • 139
2 votes
0 answers
94 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 ...
Saad's user avatar
  • 121