Questions tagged [networks]

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10
votes
4answers
725 views

How can I build a protein network pathway from a gene expression quantification file?

Assume I have found the top 0.01% most frequent genes from a gene expression file. Let's say, these are 10 genes and I want to study the protein protein interactions, the protein network and pathway....
10
votes
1answer
1k views

How to manipulate protein interaction network from String database in R?

How can I manipulate protein-interaction network graph from the String database using STRINGdb bioconductor package and R? I have downloaded the whole graph for ...
7
votes
2answers
127 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 ...
7
votes
1answer
95 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 ...
6
votes
2answers
1k views

How to select a cutoff for interaction confidence in STRINGdb?

I have a list of 100 genes that are called as hits in a genetic screening. I want to have a network of the interactions between the proteins of these 100 genes. I am using both STRINGdb web and its R ...
6
votes
3answers
250 views

Secretome and membrane receptor profiles

I am looking the secretome profile and the membrane receptor profile for a given cell type. In my specific case, this should be the secretome and outer membrane receptor profiles of dorsal root ...
6
votes
1answer
2k views

How to select a power for a scale-free topology network

In a weighted gene co-expression network analysis (using WGCNA), the soft-threshold power is recommended as a noise filtering. It consists on raising the correlation to a certain number. To decide ...
5
votes
1answer
651 views

What are the ways to process a list of differentially expressed genes?

We are studying six different human macrophage/dendritic cell types isolated from healthy skin. They all differ from each other in a few cell surface markers. We are interested in the characteristics ...
5
votes
1answer
37 views

How to query a network for a bacterium, specifically Streptomyces caatingaensis or Streptomyces thioluteus?

I have a list of gene/protein IDs and I could not query a network using String, BioGrid, Intact and IIS, for Streptomyces thioluteus. The bacteria I am working with is the Streptomyces caatingaensis. ...
4
votes
3answers
368 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 ...
4
votes
1answer
95 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 ...
4
votes
1answer
88 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 ...
4
votes
1answer
69 views

Using signal peptide and the expression levels of signal recognition particle in secretome analysis

I have not found any work which investigates assessment of differences in levels of secreted proteins by taking advantage of differential expression of the genes which mediate the secretory pathway. ...
4
votes
1answer
75 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 ...
3
votes
1answer
238 views

How to simulate biological pathways?

I would like to simulate a biological pathway in Matlab, Mathematica or Python. To study the response of the pathway using Control Theory. Is there a standard way to simulate pathways by using ...
3
votes
2answers
232 views

help with CRCmapper

I'm using CRCmapper on my data. There are several modules in the tool. I've used exactly instructed in the usage. Commands used: ...
3
votes
2answers
76 views

Can gene co-expression networks be used to help identify differentially expressed genes?

In my RNAseq dataset of differentiated stem-cell lines, some samples have far fewer significantly differentially expressed genes than others. QC shows that this is because there are way fewer reads ...
3
votes
1answer
49 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 ...
3
votes
1answer
112 views

Building network for biomarker interaction analysis

I am looking for advice on how to best approach a problem I am faced with. I have a dataset of numerous degradative biomarkers, clinical information and various other measures (from clinical trials)....
2
votes
2answers
45 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 ...
2
votes
1answer
51 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, ...
2
votes
1answer
88 views

Link Prediction in Bipartite Networks between biological pathways and drugs

Currently I'm building a big matrix (using microarray, mass spectrometry, RNAseq data) that consist by pathways (rows) and treatment/drugs (columns). The values of that matrix are scores that ...
2
votes
1answer
51 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 ...
2
votes
1answer
136 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 ...
2
votes
1answer
54 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 ...
2
votes
1answer
179 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 ...
2
votes
1answer
472 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. Example: I just feel like there's got to be a better, more time effective way to do this.
2
votes
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 ...
1
vote
1answer
192 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?
1
vote
1answer
410 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 ...
1
vote
1answer
45 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.
1
vote
1answer
103 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-...
1
vote
1answer
46 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 ...
1
vote
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
vote
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
vote
2answers
32 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 ...
1
vote
1answer
46 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, ...
1
vote
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
vote
0answers
44 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 ...
1
vote
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
vote
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
vote
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
vote
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
votes
1answer
770 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 ...
0
votes
1answer
126 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 ...
0
votes
1answer
31 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 ...
0
votes
1answer
50 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 ...
0
votes
1answer
157 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 ...
0
votes
1answer
56 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 ...
0
votes
1answer
31 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 ...