Questions tagged [pathway]

This is a tag for molecular pathways in an organism, their representation, relationships, functions and databases storing said information.

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How to represent pathways as mathematical graphs?

I would like to construct a mathematical graph: $G = (E,V, w(E))$ a graph with vertices, edges with weight on them based on a KEGG pathway. Is there a way to do that with existing tools? If not I ...
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1answer
37 views

Parsing MSigDB Supplementary Collections

MSigDB recently added Supplementary Collections. The formatting is similar to the original MSigDB gene sets, but there is an additional metadata.txt file (link). ...
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1answer
18 views

How to map selected genes to Metabolic pathway Maps

I have a selected Arabidopsis Genome Initiative (AGI) list for RNA seq and proteomics data, how can I map them to metabolic pathway maps to vilualize(e.g. TCA cycle / FA / Photosynthesis) in KEGG or ...
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62 views

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

I am working with a gene cluster found in several species. The genes involved are pretty much the same, with the odd insertion, but they can be often found in different orientations. So, I can't just ...
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13 views

Statistics in EGSEA

I am not sure if this question should be posted here or cross validated so please move if it is not appropriate. I am planning to use ensemble of gene set enrichment analysis and trying to understand ...
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39 views

Number of reactions per metabolic pathway

What is the quickest way to calculate the number of chemical reactions present in each pathway for a given organism and which online database (kegg, metacyc,reactome..) is more helpful/reliable for ...
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Cannot use .owl files downloaded in PANTHER with paxtoolsr functions

I am trying to transform a PANTHER pathway into a GSEA-appropriate format. For this, I am trying to execute the following code taken from paxtoolsr documentation ...
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72 views

Question about enrichment score (ES) and NES from GSEA

I have two results from separated two GSEA runs, and i want to know which sample has the most enrichment about specific pathway (gene set). Can I use ES (or NES) from two different GSEA analysis ...
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1answer
77 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 ...
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1answer
78 views

How do I perform a pathway related grouping of genes?

I have a list of gene names from the analysis of my mouse single seq data. I want to perform a simple grouping of the genes based on the pathways to which they belong or pathways through which they ...
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2answers
173 views

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

I would like to make a chord plot from my data. I have a list of genes that according to my experiments are divided into 64 clusters of enrichment pattern. I would combine my 64 clusters with a ...
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Pathway plot in GeneTrail data base

So I'm doing a pathway analysis using GeneTrail database. One thing I am not able to get is this similarity measure being calculated and plotted: I want to know how this is being made, what is the ...
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1answer
41 views

size of the pathways for analysis and filtration

I have recently started working on a substance's effect on a cell line in different dosages. for this, there is a tool called bmdexpress2 that I am using. Its input is the normalized counts from ...
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3answers
728 views

Pathway level analysis of single-cell gene expression

I'm looking for single-cell specific methods to construct (using gene expression data) new features that express pathway "level" or "activity", and then use these for clustering cells. One example ...
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39 views

How to create a pathway knockout using the JavaScript library ESCHER?

I want to create my own pathway with a custom knockout function using ESCHER. Consider the pathway knockout link. As you can see by clicking the reaction the color changes and the text with the html/...
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1answer
89 views

Classification (supervised learning) of expression data on pathway level

I was wondering if there is any way to apply classification algorithms (e.g random forest) on microarray data but not using the genes as predictors/features but the pathway they belong to. The thing ...
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177 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 ...
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45 views

Pathifier bioconductor package recommends to use technical noise for an argument. How to determine it?

I'm running the pathifier approach against C2 pathway curated database for a specific microarray dataset. As I was reading the documentation of the pathifier, in order to configure it properly for ...
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78 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 ...
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321 views

Comparison of gene set enrichment statistics

I am performing a gene set enrichment analysis to determine if particular gene sets are coherently up- or down-regulated. I have seen several statistics for computing a p-value of GSEA-style ...
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2answers
84 views

EMT/EMT-like processes in bioinformatics to study cancer progression

First I am not sure why, but it seems EMT can be used to infer the status of cancer progression. What kind of databases are there for the EMT process in the context of cancer? I saw this book which ...
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1k views

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

Note: this question has also been asked on Biostars I need the get the list of gene names involved in glycolysis (to put an example). Not manually, I need to do this in a script. Ideally with Python. ...
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1answer
88 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)....
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96 views

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

I have some difficulties to understand/interpret the pathway map and how a gene-gene interaction list or DNA sequencing can map into pathways. In addition what's the difference between MARK/ERK ...
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602 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....
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302 views

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

I have perform an enrichment analysis to a cluster of genes. The output is a list of pathways and their p-value (the pathways are selected because p-value < 0.05). The list is still quite long, so ...