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1,789 results • Page 2 of 36

Hello, I have trouble understanding one of the most important GSEA metrics: the signal strength. According to the documentation (http://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm...in the list and Nh is the number of genes in the gene set. This formula is also implemented in the GSEA R package (https://github.com/hxin/gsea/blob/master/R/gsea.R): signal.strength[i] <-…

GSEA

updated 7.0 years ago • Tom_L

Hi! I need to run a GSEA analysis on distinct lists of pre-ranked DEG, as well as diverse lists of gene sets obtained from MSigDB. To run the analysis...using one pre-ranked list and one gene set, the code is: fgsea_results <- fgsea(kegg.db, #Gene set b, #List of pre-ranked DEG minSize = 15, …

RNA-Seq GSEA loops R

updated 3.6 years ago • rodolfo.peacewalker

Hello all, I am doing GSEA analysis. I have done with human successfully. However, this time, I am trying to run with my mouse gene. I realized that these...are annotated with only human.. I downloaded the msigDB for mouse from genepattern website. However, GSEA program didn't allow me to use this downloaded data for my analysis... Could you please someone help me with this? I am creating...…

GSEA mouse

updated 17 months ago • illinois.ks

I've gone ahead and conducted a enrichment analysis using each of the gene sets separately through GSEA (and a background signature set I am interested in.) But is there anyway to try this with the overlapping gene-set? Because...GSEA requires one fold change value per gene, I'm not quite sure how this would work. Thanks

R GSEA

updated 3.4 years ago • bioinformatics2020

Hi, I'm interested gene ranked list comparison, these lists come from a DEG analysis (log2 ordered). Normally I would select DEG as gene sets (up or down...from one list and through GSEA I would test for enrichment against a the other pre-ranked list. In this case I would like to compare two full ordered (log2...list must be weighted, is more important that extremes of the list look alike th…

rank comparison

updated 5.0 years ago • Folder40g

peaks compared to a control using MACS2 and annotated them using Homer. I then try to perform pre-ranked GSEA. I only have positive values in my ranking, but I also get negative enrichment so I think GSEA is treating the genes...option rather than 'weighted' and it doesn't do it. Also, what would be the best scoring for pre-ranking? I have fold enrichment, peak score, q-value, p-value and pileu…

ChIP-Seq macs2 gsea

updated 4.1 years ago • sonark

Does anybody know how to extract results(rank list plus running scores for each enriched gene set) from GSEA using clusterProfiler so i can manually visualize them

updated 2.7 years ago • zhen.zhang

Hi all For non-RNA-seq data such as ATAC-seq or ChIP-seq, is there a way to perform pre-ranked GSEA that is not an ORA? GREAT/rGREAT and chipenrich seem to be popular tools for these epigenomics studies but to my...Preferably, I would like to perform differential enrichment of pathways where I can provide a pre-ranked gene list going down from upregulated in Treatment A to upregulated in Tr…

ATAC-seq GSEA

updated 4 months ago • Orange

I'm using `GSEA` function to perform enrichment analysis on my pre-ranked gene list. The function takes only genes sorted in decreasing...during DESeq2 testing or just by multiplying DESeq2 statistics by -1) I get substantially different GSEA results. **Is this behaviour expected?**. If so, **Can I perform separate tests for sets enriched in each condition?** (I think the...desktop version of GS…

GSEA clusterProfiler DESeq2

updated 3.1 years ago • hibernicah

Hi everyone, I want to run GSEA with my RNA-seq data using fgsea Bioconductor package (http://www.bioconductor.org/packages/release/bioc/vignettes...fgsea/inst/doc/fgsea-tutorial.html). What metric for gene ranking should I use? Should it be absolute log fold changes or not? In the example, provided by fgsea, they use not absolute log

GSEA RNA-Seq

updated 5.7 years ago • chipolino

Hi! I am trying to perform a GSEA preranked analysis from a paired RNAseq analysis, and I have 2 questions: - When the DESeq2 analysis is performed, a lot...Hi! I am trying to perform a GSEA preranked analysis from a paired RNAseq analysis, and I have 2 questions: - When the DESeq2 analysis is performed, a lot of genes include NAs values inside the dataframe, in the columns of Log2FC, padj, e…

DESeq2 GSEA RNA-seq Preranked

updated 3.6 years ago • rafaelsolersanblas

The GSEA manual states that the signal2noise ranking metric should be used only in case of 3+ samples per condition. What is the

gsea RNA-Seq

updated 6.3 years ago • bipin

I have done a RNA-seq analysis using Galaxy and my next step would be GSEA. Because it's a RNA-seq I need to pre-rank the gene list. I know that there are (at least?!) [two valid methods][1]: 1) use signed p-value...same p_value (for example p_value=0.00005), so with the same metric. That's not very useful for a ranking. How can I fix it? About the 2nd method it's not clear to me and I didn't f…

GSEA RNA-Seq preranking

updated 6.5 years ago • Doom

Using Limma, I calculated the differential expression for all 20,000 genes, and performed a pre-ranked GSEA. I now have ~700 gene sets that are depleted by Drug A, and ~800 gene sets that are depleted by Drug B (FDR<0.05). There...are ~280 gene sets that are depleted by both Drug A and Drug B. **Taking the pre-ranked GSEA output, how can I meaningfully compare these 280 gene sets deplete…

GSEA microarray

updated 6.2 years ago • shawn.w.foley

I have done the diffrential gene expression for stages , i did the GSEA for the same as one of my comparison i had made is Normal Stem cell vs leukemic stem cells ,so i have few doubts ,one of them...YES" while other set of genes says "NO" one of the pathway from HALLMARK used for my analysis [GSEA][1] NAME PROBE GENE SYMBOL GENE_TITLE RANK IN GENE LIST RANK METRIC SCORE RUNNING ES CORE E…

RNA-Seq gene

updated 5.8 years ago • krushnach80

Hi! I recently did a GSEA using ClusterProfiler with the gseKEGG function. As input data I used a gene list (output from DESeq2, not filtered by...change or p value) with the KEGG number for each gene and a metric for ranking the genes calculated with sign(log2foldChange) * -log10(p-value). A) First I used the DESeq2 output from "control vs mutant...mutant contrast" (I saw it is not exactly rev…

ClusterProfiler gseKEGG

updated 6 weeks ago • milkyway

gene expression differences between endometriosis patients with and without recurrence. We have a ranked gene list from the microarray results and we want to analyse it and do a pathway enrichment to elucidate which pathways...are most affected. We tried to do g:Profiler and then used EnrichmentMap with the not-ranked list of genes and the results were not good enough. Then we uploaded the ranked…

enrichment analysis

updated 2.4 years ago • sandra.taboada

I have a problem in understanding GSEA-InContext background set source of knowledge. In the main paper the authors say : *The background experiments are defined...by compiling their own experiments or leveraging a subset or the full set of the 442 pre-compiled ranked list supplied here.* I am not sure how in my datasets I can reproduce such background set. If anybody has ever worked with

gsea preranked gseapy gene

updated 19 months ago • Negara

Dear community, i have knockout mouse and performed total RNA seq analysis comparing knockout with wildtype mice. Now I have a list of about 13000 genes. There is an inhibitor of this protein and it was used in patients. Authors also performed RNA seq analysis and published a list of genes, which are differentially expressed under treatment of this inhibitor. To compare published Data with my tra…

RNA-Seq GSEA

updated 3.9 years ago • Fedo

Hi! I started to work with RNA-seq and I would like to make a GSEA analysis. I use the Cluster profiler package to do the GSEA analysis, with the `gseGO`. I get my results and everything works...Hi! I started to work with RNA-seq and I would like to make a GSEA analysis. I use the Cluster profiler package to do the GSEA analysis, with the `gseGO`. I get my results and everything works fine, b…

GSEA clusterprofiler R

updated 2.2 years ago • Pahi

respective GOs. Anyone can suggest me a tool or package to perform a gene set enrichment analysis (GSEA) on a subset of these genes that are ranked according to their p-values? Please suggest freely available software (not like

Tool to perform GSEA on mapped genes

updated 5.0 years ago • arash.iranzadeh1980

I am doing a Preranked GSEA Analysis on the output of a differential expression analysis (genes ranked by sign(shrunken lfc) * -log10(pvalue) ). I notice...that when I feed the exact same files into GSEA, it can give me fairly different FDRs. For example, when I ran the analysis the first time, it said it detected "32 gene sets...are significantly enriched at FDR < 25%". I know that the…

GSEA GO

updated 5.2 years ago • Kristin Muench

using the edgeR method which is included in the TCGAbiolinks package. I now want to perform a GSEA analysis using the GSEA desktop software, in order to see which pathways and GO terms are enriched. I have two options: I...data with each column being a sample and provide the phenotype file, or I could do a preranked GSEA providing the list of differentially expressed genes ranked by logFC. I'm …

RNA-Seq GSEA

updated 3.3 years ago • emibaffo

My big apology, but really appreciate if you can read and explain. I have been reading paper on GSEA from broad institute https://www.pnas.org/content/102/43/15545 and trying to uderstand the concept of statistics in...understood. Assum I have RNASeq data from two groups of treated and unterated tumour. To perform the GSEA, we input the GSEA software the normalized count of all genes, the algor…

GSEA

updated 24 months ago • synat.keam

As part of a larger project I've implemented GSEA in Matlab. I want to test my code by comparing my output - p-values for KEGG pathways say, with another implementation. In...As part of a larger project I've implemented GSEA in Matlab. I want to test my code by comparing my output - p-values for KEGG pathways say, with another implementation. In my...implementation the GSEA algorithm starts f…

gsea enrichment transcriptomics

updated 6.0 years ago • rachel.cavill

I have been reading about GSEA and functional enrichment, and I am confused about how to do GSEA. I know that there is a software, but R packages like clusterProfiler...and gprofiler2 also let us do the GSEA analysis. So, what is the difference between these and how do we decide if we want to do the enrichment on the software or

enrichment RNA-Seq R GSEA functional

updated 22 months ago • estafana.t98

I am working on R markdown. I got the GSEA result. I am using Clusterprofiler R package. I have 927 upregulated gene sets that have NES values equal to or greater...I am working on R markdown. I got the GSEA result. I am using Clusterprofiler R package. I have 927 upregulated gene sets that have NES values equal to or greater than +2. I have 563 downregulated gene sets that have NES values eq…

Ontology GO GSEA

updated 11 months ago • shakyaram079

Hi everyone, I am trying to analyse some mRNA-Seq data that I have generated using GSEA. I am able to generate the data using the GSEA application, but I was wondering if there was a method to carry out the traditional...GSEA in R, to streamline the analysis/data presentation. It appears that most of the packages for GSEA that I have found are more...similar to GSEA Preranked, which I would pr…

R RNA-Seq GSEA

updated 11 months ago • james.zhang20

of methods of GSEA analysis, including overrepresentation analysis, univariate methods, multivariate methods, as well as extensions...of GSEA analysis, such as network-based GSEA, and single-sample GSEA. Finally, you will also learn downstream processing of GSEA...results, including efficiently visualizing the massive GSEA results, clustering, and simplifying GSEA results via various methods. In …

Bioconductor R GSEA GeneSetEnrichmentAnalysis

updated 16 months ago • carlopecoraro2

Here is a new tool for Gene Ranking and differential expression analysis of RNA-Seq Data via [Discriminant Non-Negative Matrix Factorization (DNMF...1]. 1. What can DNMF do? Gene ranks of RNA-seq for gene set enrichment analysis ([GSEA][2]) due to there are no built-in ranking methods for RNA-seq data. Or other...tools requiring gene ranks. Additionally, differential expression analysis of RNA…

gene-ranking NMF gsea RNA-Seq DNMF

updated 2.5 years ago • Zhilong Jia

question regarding the heatmap of the top 50 features for each phenotype in dataset generated by GSEA. I wonder is it also called differentially expressed genes? The heat map showed some genes are clearly up- and down-regulated...I got from EdgeR. Noted, I used normalized count value (CPM) from TMM method in edgeR as input for ranked gene list in GSEA. Please help me elaborate, thank you in adv…

GSEA EdgeR Heatmap DEGs

updated 24 months ago • TM

what the collapse option does with rna-seq data and if I should be using it. I'm using the GSEA 4.0.3 to analyze rna-seq data I was able follow the instructions [here][1] with the hallmarks collection and Mouse_ENSEMBL_Gene_ID_MSigDB.vX.chip...and it ran and I thought everything had worked perfectly. But then I also tried to run GSEA preranked with the -log10 of pvalues from sleuth and got erro…

rna-seq

updated 4.0 years ago • thegeneral

a paper [Recurrently deregulated lncRNAs in hepatocellular carcinoma][1] in which they have done GSEA using lncRNA expression data. Check the Figure 3a and 3b, And the figure looks like below: ![enter image description here...2] In the Methods section I see the following information: We used GSEA (v2.0.13) to assess enrichment of sets of recurrently deregulated lncRNAs in other data sets. GSEA…

RNA-Seq r gsea lncrna

updated 4.0 years ago • newbie

Hello, I have ranked mouse gene list and gmt files that contain upper case gene names. Can I just change the mouse symbol gene name to upper...case to run GSEA using gmt files that contain upper case gene names? Thanks a lot

GSEA gmt

updated 2.2 years ago • lidan0001

I try to do GSEA. Therefore, I downloaded mRNA data files(GCT) from firebrowse. Then i did ranknormalization by using Gene pattern. After...tumor and normal tissue RNA data are mixing in. So can i exclude the normal tissue data ?? Then do GSEA?? or Include the tumor and normal tissue RNA data. Then do GSEA?? Thank for reading my question Pleas give comments please

rna-seq RNA-Seq

updated 6.4 years ago • mysskks

Hi, I have expression values for around 20,000 genes in 100 different individuals. I need to rank these genes for association with the following parameters: 1) the genotype at a certain locus. This genotype can be homozygous...individual (integer value that ranges from 0 to around 30). What are the best statistics for these rankings? Thanks a lot

gsea gene expression

updated 8.9 years ago • Selenocysteine

analysis to identify biological processes associated with the treatment, so you'll need some way of ranking the genes. In this scenario, how would you aggregate the gene expression changes/pvalues across the three contrasts...and what calculated statistic should you use to rank the consensus genes? Thanks

RNA-Seq meta-analysis GSEA

updated 3.8 years ago • monovich

Hello, I am trying to implement a R function which does the GSEA. I read many papers related to this method and each of them tries to destroy the other and show a better performance of...Hello, I am trying to implement a R function which does the GSEA. I read many papers related to this method and each of them tries to destroy the other and show a better performance of its...they say &gt…

GSEA R Microarray

updated 2.0 years ago • Mo

interpreting error 1001 (After pruning, none of the gene sets passed size thresholds) when using the GSEA 3.0 desktop app. My data consists of DESeq2 analyzed polyA-enriched RNA-seq reads. I ranked my data by a significance score...with the nomenclature of the MSigDB. This data table consisting of gene symbols (column 1) and ranked significance scores (column 2) was exported into a tab-delimite…

RNA-Seq GSEA gene genome

updated 4.8 years ago • limjustinj

Hello Biostars, Can anyone tell me how to prepare input data set for GSEA after Differential Gene Expression Analysis by DESeq2? How will I rank the genes? Should I rank based on log2FC or Adjusted...P value? Is there any way to generate a GSEA ready data directly from DESeq2?. I was using topGo for gene ontology enrichment analysis before and recently came across...GSEA. Which one is better GO …

RNA-Seq DESeq2 geneontology GSEA

updated 5.5 years ago • Sreeraj Thamban

of Deferentially Expressed Genes obtained from DESeq2. Now I would like to do further analysis using GSEA. I prepared the rank file by using the code below: x <- read.csv("DEG-B_vs_A.csv") attach(x) x$fcSign=sign(log2FoldChange) x$logP...gt; 4 AT1G01240 -7.978849 > 5 AT1G01280 3.131964 1.) Now when I try to load this file on GSEA 3.0, it shows some error: &gt…

RNA-Seq next-gen

updated 5.1 years ago • umeshtanwar2

me to blast against all metazoa because otherwise i would get very few annotations. I want to do a GSEA analysis to compare my results with gene sets related to my research interest. The problem I am having now is with the...GSEA chip annotation since their database is limited to human and mouse. On the website of GSEA it states: GSEA uses the selected...the gene descriptions from the expressio…

RNA-Seq GSEA enrichment analysis

updated 3.3 years ago • natasha.tilich

I am wondering when it is appropriate to use GSEA vs pathway enrichment analysis in single cell RNA sequencing analysis. I have generated markers lists for my clusters...0.25 and min.pct = 0.2. According to Reimand et al. 2019 (Nature Protocols; 14:482-517), partial ranked gene lists should be analyzed using pathway enrichment analysis. How does this apply to single cell data? Thank you

GSEA pathway scRNAseq

updated 3.1 years ago • aa123

I have RNA-seq count data and I have already identifying differentially expressed genes DEGs. and Protein-protein interaction analysis for those DEGs. I would like to perform GSEA for comparison with the previous analysis. and I am confused about what should I do 1. Should I take all genes in the RNA-seq...genes DEGs. and Protein-protein interaction analysis for those DEGs. I would like to per…

DEGs GSEA RNA-seq

updated 5 months ago • 1961012

The Gene Set Enrichment Algorithm, outlined in this paper, http://www.broadinstitute.org/gsea/doc/subramanian_tamayo_gsea_pnas.pdf, refers often to a "random walk" used to traverse the ranked list L of gene-to-phenotype...do in the paper does not look like a random walk at all. It seems to me that they traverse the ranked list L sequentially, from rank 1 (highest correlation) onwards. I was won…

updated 11.1 years ago • rolyata47

Hi, I want to do GSEA between two categories of tumors.I am interested in using hypergeometric tool in GSEA. I am not able to find if its present...Also,I want to do enrichment only for down regulated genes with logfoldchange < -2.Can I do GSEA preranked? http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/FAQ#What_is_the_difference_between_GSEA_and_an_overlap_statistic_.2…

gsea RNA-Seq

updated 17 months ago • Ron

I have a very naive question and could not find a proper answer on broad GSEA web page too, I am most of us may know the answer. When we perform GSEA analysis in some case we have negative normalized enrichment

GSEA interpretation

updated 2.0 years ago • kanwarjag

Does anyone know how to download and install the R-GSEA package? If I try to register via http://www.broadinstitute.org/cancer/software/gsea/software/software_index.html

updated 21 months ago • kynnjo

What does it mean when all SNPs identified by discoSnp have rank = 0? Does it mean that the data is noisy and ranking does not work well

discoSnp

updated 6.3 years ago • bellbrown1396

I want to run GSEA on my DEGs from scRNA-seq analysis, which contains gene name, logFC, p-value, adjusted p-value data. However, in the Broad Institute...GSEA tutorial on how to format input files, their file contains gene expression across multiple samples but not DEGs. Is there...any way to use DEGs input in GSEA software? If not, are there any other gsea tools that can calculate enrichment sc…

gsea RNA-Seq scRNA-seq Seurat

updated 3.4 years ago • biostarukha

1,789 results • Page 2 of 36

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