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9 votes
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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
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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6 votes
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Classification (supervised learning) of expression data on pathway level

Have a look at the GSVA package. It allows to convert a matrix with genes x Samples to a pathways x Samples using several ...
llrs's user avatar
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6 votes
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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
  • 76
6 votes

How can I extract gene names for a metabolic pathway from KEGG?

using the REST API of togows: one can fetch a json structure of the genes associated to a kegg pathway. eg: http://togows.org/entry/kegg-pathway/hsa00010/genes.json ...
Pierre's user avatar
  • 1,566
6 votes

How can I extract gene names for a metabolic pathway from KEGG?

I whipped this little script up using the KEGG API: ...
terdon's user avatar
  • 10.4k
4 votes

How to select the most representative pathways from a gene enrichment analysis?

This sounds like something that might be amenable to a clustered heatmap plot, or a correlation matrix plot, or something similar. Have you looked at a correlation matrix of the dice coefficient ...
gringer's user avatar
  • 14.7k
4 votes

Comparison of gene set enrichment statistics

I assume that you are talking about the implementation of these methods in the limma package. Otherwise this answer does not apply. I think that your questions can be answered with some simulations ...
llrs's user avatar
  • 4,713
4 votes

size of the pathways for analysis and filtration

The problem here is that any one GO term with a small number of members is unlikely to include any differentially expressed genes by chance, but if you test a large number of GO terms, some of them ...
heathobrien's user avatar
  • 1,816
3 votes
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Pathway plot in GeneTrail data base

This is a a symmetric matrix with the pathways in both axes. So for each pair a similarity index is calculated (usually it takes into account the number of genes in each pathway and the total number ...
llrs's user avatar
  • 4,713
3 votes

How can I extract gene names for a metabolic pathway from KEGG?

Answers from Biostars: GeneSCF 'prepare_database' module will extract all the pathways with corresponding genes as simple table format in plain text file. Check 'Two step process' (sub-heading) from ...
3 votes
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How to select the most representative pathways from a gene enrichment analysis?

One way to group similar significant pathways, is to quantify how many genes overlap between the pathways, and then use this in clustering (heatmap). I have made a tool in R which calculates the ...
benn's user avatar
  • 3,591
2 votes

How to select the most representative pathways from a gene enrichment analysis?

If you're happy with a more confident ranking of the most representative gene sets, rather than necessarily cutting down the list, you might try EGSEA. It uses an ensemble approach to give a ranking ...
Scott Gigante's user avatar
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

How can I find the relevant pathway map from gene-gene or protein-protein interaction list?

As you alluded to in your question, KEGG does provide a curated set of enzyme and metabolite information. This information can be parsed and used to create a network that you can analyze to look at ...
G_Hannigan's user avatar
2 votes

How can I find the relevant pathway map from gene-gene or protein-protein interaction list?

See a project like Plant reactome, where they infer the pathways of all sequenced plant genomes using orthology to well annotated species. http://plantreactome.gramene.org/
Dan's user avatar
  • 612
2 votes
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EMT/EMT-like processes in bioinformatics to study cancer progression

EMT describe cells' change in their state from being epithelial to the mesenchymal class. So, if a cancer cell line is gaining properties that allow it to move, it might reach the metastasis phase, ...
llrs's user avatar
  • 4,713
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

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

Pathway level analysis of single-cell gene expression

Package Hipathia allows you to compute a value of "activity" for each pathway and each cell, so that the matrix of gene expression is transformed into a matrix of pathway activity. You can use this ...
Marta R. Hidalgo's user avatar
2 votes

Parsing MSigDB Supplementary Collections

If you want to separate each set, you can do something like this ...
fra's user avatar
  • 567
2 votes
Accepted

How do I perform a pathway related grouping of genes?

The DAVID tool is always interesting, and easy to try: https://david.ncifcrf.gov/gene2gene.jsp You submit a list of genes, it uses several different annotation databases to annotate the gene list, ...
Jay Moore's user avatar
  • 1,012
2 votes

How to cluster the human genes by pathways/system-biology/metabolic properties?

To measure if two genes are functional similar I developed the BioCor package. It calculates a similarity score between genes by the measuring the amount of pathways shared. However, it doesn't take ...
llrs's user avatar
  • 4,713
2 votes

Turning GMT file into data frame so that third column is comma seperated

I used the unite function from tidyr but first I read the gmt file in as a data table using the read.delim function (with header set to False). Then I used unite: ...
tacrolimus's user avatar
2 votes

Is the potential skewing of FDR and ranking of gene set analysis with gene sets with hierarchical structure a concern?

Statisticians might kill me for it but I've always filtered long and redundant geneset lists to only contain what remotely makes biological sense in my setup. If I am investigating leukocyte ...
ATpoint's user avatar
  • 1,440
2 votes
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Is the potential skewing of FDR and ranking of gene set analysis with gene sets with hierarchical structure a concern?

This is actually a known problem in the correction of nominal p-values in over-representation analyses that use the Gene Ontology categories (commonly but misleadingly called "GO enrichment" ...
gdagstn's user avatar
  • 131
2 votes
Accepted

How to prove correlation between gene expression and functions using omics data in bioinformatics?

In general terms data mining is needed, then supervised learning and finally ODE, because you are performing DE against enzyme kinetics and thats doable, but you'll need a lot of biochemical knowledge....
M__'s user avatar
  • 12.8k
1 vote

How to cluster the human genes by pathways/system-biology/metabolic properties?

Production of a chord diagram is described in detail here. You use the R package with either, library(chorddiag) library (circulize) The first level clusters ...
M__'s user avatar
  • 12.8k
1 vote
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How to map selected genes to Metabolic pathway Maps

KEGG has a webtool for this, KEGG Mapper. You can just copy-paste your gene ids in there and see how your pathways are colored.
benn's user avatar
  • 3,591
1 vote

Are there any resources for calculating / representing evolutionary relationships within gene clusters?

Firstly you wanted a webserver to build a tree, ok, I would use PhyML server. The good thing is that with only 22 taxa the calculations are easily doable. What I'm assuming is you can map your ...
M__'s user avatar
  • 12.8k

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