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10 votes

Are gene names same across species?

Gene names are not consistent across species. Most of the time genes are automatically annotated and the algorithms try to give names that are similar to their matches in other organisms, but not ...
gringer's user avatar
  • 14.3k
9 votes
Accepted

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

There are multiple ways to do this, and multiple protein interaction databases besides the ones you mentioned, such as BioGRID or IntAct. Interaction databases are different in how interactions are ...
Iakov Davydov's user avatar
7 votes
Accepted

How to simulate biological pathways?

In matlab this can be done using the SimBiology toolbox. In mathematica this can be done using the SystemModeler. In python there are multiple packages, e.g. (in no particular order) PySB, Tellurium, ...
HasHPIT's user avatar
  • 86
7 votes
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What are the ways to process a list of differentially expressed genes?

You originally had asked a very broad question, so I'll try to demonstrate why that is such a hard question to answer. I've done two fairly large differential analysis studies (and a few smaller ones) ...
gringer's user avatar
  • 14.3k
6 votes

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

Many interaction databases now work with PSI format files. Most of the main databases can do this and the EBI has set up PSICQUIC View, a very useful page where you can query multiple databases at ...
terdon's user avatar
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5 votes
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How to select a cutoff for interaction confidence in STRINGdb?

I have used STRING pretty heavily, and have compared it to various other databases of protein interactions and signaling pathways. I do feel like it has a lot of quality interaction annotations, but ...
woemler's user avatar
  • 439
5 votes

How to select a cutoff for interaction confidence in STRINGdb?

This depends on what you are trying to do and whether you value specificity over sensitivity. We can't tell you since it is entirely dependent on the biological question you want to answer. However, I ...
terdon's user avatar
  • 10.2k
4 votes
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How to manipulate protein interaction network from String database in R?

I think the easiest way is to download the graph using STRINGdb. ...
Iakov Davydov's user avatar
4 votes
Accepted

Are gene names same across species?

You could try using BioMart in Ensembl Metazoa. Filter by your list of gene names in honeybee, then get the fly homologues as attributes. The homologues are calculated by sequence comparison and ...
Emily_Ensembl's user avatar
4 votes

Network comparison of single cells (from sequencing data)

You can't build a network of a single cell only with the expression of a single cell. You either need previous known interactions or pathways or you need to use several cells/samples. If you use ...
llrs's user avatar
  • 4,713
4 votes

Visualize similar interactions in two homologous networks

An easy way to visualize this is to make a tab-delimited table that contains edge information for both species and both networks, color the edges depending on the species, and make the thickness and ...
conchoecia's user avatar
  • 3,181
3 votes

How to read gene regulatory network edge list files?

You can read about it on the website, the last column is the Log likelihood scores (LLS) between the genes in the first two columns. An LLS of 0 means not better than random link. On the website they ...
benn's user avatar
  • 3,571
3 votes
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Populations genetics and dynamics of bacteria on a Graph

I assume you are simulating a null distribution. Are you investigation recombination?? My main advice is to use population genetic terminology rather than geomometry to describe your simulation (e.g. ...
M__'s user avatar
  • 12.5k
3 votes

Can you style network visualizations of directed graphs using NETWULF?

I'm the author of gravis, an open-source package for interactive graph visualization in Python. It allows to draw directed graphs from NetworkX and the resulting visualization can be modified by user ...
Robert Haas's user avatar
3 votes
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How to find closely related genes for a specific gene from WGCNA modules?

The simplest way is to re-calculate (or load, if saved) the TOM matrix and find the genes with the highest TOM to MALAT1. If you have enough RAM to carry out WGCNA in a single block, you can use ...
Peter Langfelder's user avatar
3 votes
Accepted

Coexpression network analysis

igraph is a serious general network theory framework for any given data science application. It permits full directionality and describes vertices (nodes), edges (...
M__'s user avatar
  • 12.5k
2 votes

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

If you run this Rscript using the gene name as an argument, you'll get a file with the pathway written to the directory. ...
jaslibra's user avatar
  • 524
2 votes

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

I would be concerned about the input data that produced these numbers. This dataset has a really odd shape with a dip at the start: ...
gringer's user avatar
  • 14.3k
2 votes

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

Co-expression network will give you an idea about the genes having similar expression patterns and the nodes will be decided on the basis of correlation scores and nothing much you will get from ...
arup's user avatar
  • 604
2 votes
Accepted

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

While you can use networks to find differentially expressed genes (see the WGCNA package, which does this) in my experience this ends up largely matching what you'd get using a traditional package ...
Devon Ryan's user avatar
  • 19.6k
2 votes

help with CRCmapper

This error came from the fact that the output of the new fimo version has an additional 'motif_alt_id' column in second position. CRCmapper has been modified to take this into account. You can find ...
Violaine Saint-André's user avatar
2 votes

help with CRCmapper

It seems that the author of CRCmapper.py wants to extract sequence_name, start, stop columns ...
ying's user avatar
  • 21
2 votes

Link Prediction in Bipartite Networks between biological pathways and drugs

I am not sure if I understood correctly how you classify the drugs. But what you attempt to do is similar to what they do here but in that article they use the drugs targeted to a molecule/pathway to ...
llrs's user avatar
  • 4,713
2 votes

Building network for biomarker interaction analysis

You can start by looking at the correlation (if data is non-parametric) of each variable with each variable of each data point you have. One thing that might change is the correlation between ...
llrs's user avatar
  • 4,713
2 votes
Accepted

Motif Discovery in Bipartite networks using Cytoscape

I have recently develop an R package (sorry not a Cytoscape solution) to deal with this kind of situations of something grouping other elements, like pathways and genes. The package is based on ...
llrs's user avatar
  • 4,713
2 votes

Visualize network (graph) using "line" layout

I'm the author of gravis, an open source package for interactive network visualization in Python. It supports many ways to influence visual properties with data, such as node size, color or location. ...
Robert Haas's user avatar
2 votes
Accepted

Visualize network (graph) using "line" layout

That plot is called an Arc diagram you can google that and use the package or program that best suits you. Here are 2 examples of the use of Arc diagrams in R: Example 1: Example 2:
Mack123456's user avatar
2 votes

How to calculate Gene Ontology terms in python

You can calculate gene ontology similarity with the GOSemSim R package (paper)(disclaimer I'm a contributor to this package). You have several similarity scores implemented, some of them are across ...
llrs's user avatar
  • 4,713
2 votes
Accepted

Compare two networks of the same genes between two species

So, you can give a try to this Cytoscape app that will allow to perform comparison between networks. This app is not specifically designed for comparing networks across different species but it will ...
gabt's user avatar
  • 348
2 votes
Accepted

Retrieving Metabolic networks from WIT Database

It seems like there are some files related to the databases at the ftp site: http://ftp.mcs.anl.gov/pub/WIT2/. The related files were last updated on 2002. I found it via searching at google: ...
llrs's user avatar
  • 4,713

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