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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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
70 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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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
107 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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1answer
32 views

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 ...
4
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1answer
39 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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2answers
443 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 ...
4
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0answers
36 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/...
5
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1answer
73 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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1answer
118 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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44 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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1answer
67 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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1answer
253 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
75 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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3answers
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. ...
3
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1answer
84 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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504 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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240 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 ...