Biostar

1,787 results • Page 1 of 36

Hi, I'm trying to run GSEA on a ranked list of genes. In other words, I'm not using expression data (instead, I'm using a list of genes ranked by the prevalence...of variants in those genes in my dataset). I can't figure out how to run GSEA using non-standard input files - either the desktop version or the R version. Each tutorial I can find details how to run...GSEA on expression files that con…

GSEA SNP variant-calling

updated 2.3 years ago • chloe.p.oconnell

If you have 2 groups(phenotypes) of sample, will [GSEA](http://software.broadinstitute.org/gsea/index.jsp) calculate 2 different gene rank list? I mean if their rank list is...the same(or reverse) their GSEA result should be the same, but the fact is not, java-GSEA will give results for each group(phenotype

GSEA

updated 4.5 years ago • MatthewP

Dear Biostars, I want to prepare the rank file for GSEA analysis based on RNA-seq results that were generated by DESeq2. I have found different recommendations...as how to create the pre-ranked gene list. The GSEA site mentions the gene list can be sorted by any value, however, other people have pointed out in this...blog that the direction of fold change is important for GSEA analysis. Now, if …

RNA-Seq GSEA

updated 20 months ago • noushin.farnoud

Dear all, I am trying to do my first pathway enrichment analysis of a ranked gene list using GSEA, as described in the relatively recent protocol published here: https://www.nature.com/articles...that I have, more or less, learned how to perform the DE analysis (using DESeq2), how to format the rank, class, gmt and expression files for GSEA, and use other tools required by the protocol. However,…

RNA-Seq GSEA Calculating ranks Enrichment analysis

updated 4.8 years ago • zlikowski

Hi I want to do GSEA preranked. I have used algorithm X (probability based algortihm) to find causal gene. Highly causal gene which causes...1) whereas less causal gene or no causal gene gives me around close to 0 probability. I want to do GSEA based on the algorithm result (rank). I learnt that people mainly do log fold or pvalue for GSEA preranked, but my case is different...that how can I …

gsea score enrichment GSEA python R

updated 18 months ago • asadrahmanms

Hi~ I would love to run pre-ranked GSEA on a list of genes. May I ask if I should input all of my genes into pre-ranked GSEA? or I should filter it based on some

gsea ranked

updated 6.9 years ago • blairzxy

Gene ranking is to ranking all the genes measured by Microarray or RNA-seq. GSEA is one of applications of gene ranking. So what else

gene ranking GSEA

updated 9.0 years ago • Zhilong Jia

Dear guys, Do you recommend to use t to rank gene or log2FC or sign(log2FC) * -log10(Pvalue) to rank gene? The fgsea use t to rank the gene. [fgsea rank gene Rscript][1] While when...different from the others like Pvalue, adj.Pvalue, etc. Aslo, when looking at the results from GSEA, it seems Pvalue is more mentationed, while not using adjusted-P value? ![enter image description…

Gene_rank GSEA

updated 5 months ago • luckyday1661

Can I use p-values in the pre-ranked file provided to GSEA? The format of the file would look like (Gene symbol -- p-value): ``` HGMGCS1 1.83E-13 TMEM97 2.14E-11 .. .. NDST4

GSEA

updated 13 months ago • jerome.lane.34

Hi! I have a preranked list of genes that I'd like to run through GSEA. These are genes that correlate with a specific antibody responses, and are results that I have received from our bioinformatician...the exact same number (either positive or negative)! How can this be and how will this affect how GSEA ranks the genes? Thanks

GSEA

updated 7.5 years ago • janders8

I'm analysing an RNA-Seq dataset and want to do preranked GSEA to find out what pathways are changing in my dataset. I've read that this type of analysis should be done using ALL the genes...or Up+drug-sensitive/down/drug-sensitive etc... I thought I would run these clusters in a pre-ranked GSEA, with the ranking statistic being the Log2FC (or some other statistic) of the control vs stimulate…

RNA-Seq GSEA

updated 3.4 years ago • James Cook

Hello everyone, I'm currently using clusterProfiler to run GSEA on my samples and I'm interested in seeing the order and ranking of **all** the genes in my given signature. While the gseaResult...of the signature under the core_enrichment column, I was wondering if there was a way to see the ranking and placements of all the genes in the given signature. Any advice regarding this would be …

R clusterProfiler GSEA

updated 4 months ago • mflab

I am doing pathway and gene ontology analysis using Gene Set Enrichment Analysis(GSEA). For the tools, you need to provide a ranked gene list, however, various papers have provide different recommendations...any literature reviews or clarification on the issue. clusterProfiler mentions fold change for ranked gene lists, so I am unsure if I would be getting "bad results" by using p-value sorting.…

GSEA GO Gene ranking RNA-Seq

updated 5.1 years ago • Gabriel

methods (please see below): could you explain me which one could be the best? And mainly why? 1- GSEA pre-ranked with all DESeq2 log2FC values (Time1 vs Time0) & pearson correlation analysis with significant NES values...ratios 3- pearson correlation analysis with significant DESeq2 log2FC values(Time1 vs Time0) & GSEA pre-ranked with correlation results (r values with p&l…

RNA-Seq GSEA ssGSEA

updated 3.9 years ago • :)

Hey y'all I'm currently trying to run GSEA using a pre-ranked gene list but I'm not sure if my input file is correctly formatted, because my results seem to be mostly...insignificant. So my input looks something like this (roughly 16,000 genes): Where my ranking statistic is the negative log of the p-Value obtained through an association test. ``` GENE neg_log_Chi_permutation

gene next-gen RNA-Seq genome software

updated 21 months ago • stevenlang123

row) and transcription factors binding sites (colums). I would like to convert this file as a Pre-ranked file and submit to GSEA. Any suggestions would be appreciated. ex: name tf1 tf2 tf3 gene1 0.8 0.4 0.2 gene2 -0.2 -0.6 -0.7 gene3

GSEA

updated 2.6 years ago • biorepine

Hi all, I have done GSEA pre-ranked on differentially expressed genes between tumors and normals. The genes have been ordered by log fold change...since GSEA pre-ranked requires an ordered list of genes. The results are outputted in the format with phenotypes as `na_pos` and `na_neg...between the 2 phenotypes based on an ordered list of genes. I understand that the normal GSEA when run on tumo…

GSEA differential-expression next-gen rna-seq

updated 23 months ago • Ron

Hi guys, I have a general question regarding the pre-ranked GSEA. I have a list of genes ranked according to the LogFC and then a list of genes that is my geneset. I would like to see...if the genes of the geneset are enriched in my ranked list. To do this, I'm running the pre-ranked GSEA. I'm not sure the meaning of NES and FDR. Which is the statistical score to

gsea

updated 4.9 years ago • elb

Greetings! I was wondering what people's thoughts are on performing a preranked GSEA type analysis on unsigned / one-sided gene statistics are? [Most of the](https://journals.plos.org/plosone/article?id=10.1371...to focus on the things like gene expression fold-change across two conditions, where a _signed_ gene ranking can be generated, e.g. - Fold-change, or, - Sign(fold-change) * -log10(P-v…

GSEA fgsea preranked unsigned one-sided

updated 4.5 years ago • keith.hughitt

to discern the unrounded values of these P-values as they are needed in order for me to produce a rank list for gene set enrichment analysis (GSEA). Any guidance on how to approached ranking these genes would be appreciated

RNA-Seq gene R

updated 6.3 years ago • Krish Srinivasan

Dear all, I am analyzing a RNA seq data and I've get through DE analysis. Now I want to do GSEA analysis. What I got: DESeq2 results. I rank the results in p-value and use the code here to generate rank file. ([How to generate...a rank file from gene expression data][1]) When I try to load this rnk file into GSEA and do analysis(Run GSEA on a pre-ranked gene list...the instruction [here][…

RNA-Seq

updated 8.0 years ago • izzy.yichao.cai

I read that very small or very large gene sets can affect the enrichment score and p values in a GSEA analysis (e.g. if there are 10 genes in a gene set vs. 100 genes in a gene set, the former would be more likely to return a significant...p value), and that's why GSEA normalizes for variations in gene set size. I'm curious if a very small or very large pre-ranked gene list can also affect

gsea enrichment p-value statistics

updated 2.8 years ago • garfield320

Hi there, I am trying to use TopGO to perform some GSEA analyses (Gene Set Enrichment Analysis). In order to do this, I have done the differential expression analysis for all...Hi there, I am trying to use TopGO to perform some GSEA analyses (Gene Set Enrichment Analysis). In order to do this, I have done the differential expression analysis for all genes...the P-values and Fold change values f…

TopGO GSEA RNA-Seq

updated 6.9 years ago • wangdp123

Dear all, I have been running GSEA, since I am very new to GSEA, I am poking around both R package clusterprofiler and the original GSEA software(GSEA_4.3.2...However while I was running the same pre-ranked gene list, I got different results from three methods (gsea, gseaGO from clusterprofiler, GSEAPreranked from broad...institute GSEA_4.3.2) With clusterprofiler, I did similar tests as this [p…

GSEA clusterprofiler RNA-seq R

updated 18 months ago • jian227

Hi there! I am following [this][1] tutorial to perform GSEA using [fgsea][2] R package. In the tutorial, DEG are ranked using `stat` variable from DESeq2. I have read in several other places...that it is common as well to rank based on fold changes, p-values, a combination of these two ... I would appreciate any guidance and comments on this regard...I am quite newbie when it comes to GSEA. Th…

GSEA

updated 23 months ago • user230613

a list of genes from DEG analysis, with p-values, FDRs, & logFCs, etc. Previously, what I do for GSEA analysis is to filter in genes with FDR < 0.25 or 0.05, rank them by logFC (in other words, pre-rank the genes by logFC), and then...do GSEA. Now I am wondering if this is a good way: * There might be too many genes (typically ~50%). Assuming usually there are 4~5 pathways..…

rna-seq next-gen gene

updated 7.1 years ago • moxu

Hi there, I’m wanting to use Broad’s PreRanked GSEA tool on a list of genes and their log2(FC) values to look for enrichment of a number of gene sets (details: FC values based...Hi there, I’m wanting to use Broad’s PreRanked GSEA tool on a list of genes and their log2(FC) values to look for enrichment of a number of gene sets (details: FC values based on...would be OK, but I want to be sure. I’d …

GSEA RNA-Seq

updated 4.9 years ago • edward_william

how to calculate the gene's correlation with phenotype in GSEA ? For example: two kinds of samples: Ctrl and Exper, GSEA will give a ranking list of genes that related the phenotype Exper...how to calculate the gene's correlation with phenotype in GSEA ? For example: two kinds of samples: Ctrl and Exper, GSEA will give a ranking list of genes that related the phenotype Exper. At the same time…

correlation gene-expression

updated 10.5 years ago • Zhilong Jia

I recently analyzed my RNA-Seq data followed by STAR-HTSeqCount-DESeq2 method and want to run these on GSEA to find correlation with certain pathways. But for the input, should I prerank the genes based on Log2FC or log(p-value) * sign_of_FC...recently analyzed my RNA-Seq data followed by STAR-HTSeqCount-DESeq2 method and want to run these on GSEA to find correlation with certain pathways. But fo…

RNA-Seq gene R GSEA next-gen

updated 6.4 years ago • langya

differential expression of the genes independently of one another, and now I would like to perform GSEA (http://software.broadinstitute.org/gsea/index.jsp) or a similar analysis on my RNA-seq data from these samples to identify...the same goal as the unanswered question found here: https://www.biostars.org/p/68895/ ). The GSEA faq says it cannot be used directly with paired samples, but that "if …

RNA-Seq rna-seq gsea

updated 4.6 years ago • bjeremy

Hi Biostars I am trying to use GSEA GUI from broad institute to do gene set analysis on RNA seq data. I have been reading many posts and researched GSEA website...Hi Biostars I am trying to use GSEA GUI from broad institute to do gene set analysis on RNA seq data. I have been reading many posts and researched GSEA website about the DEseq2->GSEA workflow and here is what I understood from…

rna-seq R GSEA DESeq2

updated 6.8 years ago • sup230

Hi I'm running GSEA on my pre-ranked genes consisting 260 differentially expressed genes following GSEA instructions, but it is obscure...for me how to set max and min size for exclude gene set. In GSEA user guide it's noticed that "defaults that are appropriate for datasets with 10,000 to 20,000 features. To change these...default values, use the Max Size and Min Size parameters on the R…

GSEA

updated 6.5 years ago • Shamim Sarhadi

an expressionSet including case and control samples, I did DEG analysis with limma, now I want to do gsea analysis for 2 phenotype , but I am hesitate about choosing above mentioned approachs and which one is more reasonable...1. gsea on total dataset including case and control 2. gsea on subset of total dataset with DEG between case and control that come...from limma toptable output 3. preRanke…

GSEA DEG

updated 8.0 years ago • Shamim Sarhadi

approach for interpreting genome-wide expression profiles" by Subramaniana et al. Here, it says ranking genes based on the expression difference, but I found in the Fig.1A that there are multiple attributes for each gene

gene enrichment

updated 6.0 years ago • jin.k.koo

I came across multiple posts regarding the pre-ranking metric for GSEA when using RNA seq data. However, there doesn't seem to be a consensus. Some of the metrics I came across...log10(p-value[**not adjusted p-val**]) - logfc shrink values from DESeq2 - Inbuilt signal2noise from GSEA. *However, this cannot be used in case of <3 replicates.* What metric do you use for ranking the genes o…

RNA-Seq gsea deseq2

updated 6.2 years ago • bipin

What are the differences between GSVA and GSEA? I got some idea from a toward data science post ([link][1]): "GSVA builds on top of GSEA where a set of genes is characterized between...two condition groups defined in the sample. GSEA works on how genes are behaving differently between the two groups defined." from my own understanding, - GSEA first analyze...the differences between…

gsea genome genetics gene gsva

updated 13 months ago • DS

Hi all, I am working with GSEA results using GSEA pre ranked. My input is list of genes with their log2foldchange as the metric . The genes with log2foldchange...were calculated using Differential expression. Now in my GSEA results. I see this pathway plot. The pathway name is RB_P130_DN.V1_DN and its description in Msigdb database is "Genes

RNA-Seq GSEA next-gen

updated 6.0 years ago • Ron

Hello everyone, I'm trying to understand how GSEA works and what I have understood so far is that in GSEA we use all the genes in our RNA-seq data set and then rank them with...I came across this statement in one of the analyses where they used GO and KEGG datasets for GSEA, generating two GSEA results folders, each for GO and KEGG. this confuses me since I haven't heard in any of the tutorial…

RNA-seq GSEA

updated 18 months ago • shahbaz.ahmed

Hello, I have performed GSEA analysis using the Broad's GSEA software. I now want to create a running enrichment score figure that includes my top 4...Hello, I have performed GSEA analysis using the Broad's GSEA software. I now want to create a running enrichment score figure that includes my top 4 gene sets using the 'enrichplot' package in R. (example picture below) However, I cannot figure o…

r enrichplot gsea visualization enrichResult

updated 7 months ago • Cortney

several tables of results from different DESeq2 runs. The next step would be to do GO enrichment or GSEA enrichment analysis. For that I would like to create a ranked list of genes for GSEAPreRanked. But I'm not sure which value...to take for the ranking. Do I use the log2FC values or the p-values, or even the adjusted p-values. I have searched in different foren and the opinions...padj)` I g…

gsea deseq2 preranked fgsea

updated 4.2 years ago • Assa Yeroslaviz

Enrichment Analysis using either the tool from Broad Institute http://software.broadinstitute.org/gsea/index.jsp or the online tool Webgestalt http://www.webgestalt.org/ Both require to prepare an input file of (*.rnk) format...that would contain gene names in one column and a corresponding rank value in the other. Here's the guideline from Broad: "Prior to conducting gene set enrichment analysis…

RNA-Seq GSEA Enrichment analysis R webgestalt

updated 4.6 years ago • o.mikh90

I understood the meaning of the positive and negative normalized enrichment scores (NES) produced by GSEA, but it just occurred to me I don't know what to expect from a gene set that is enriched both at high and low ranks. For example...of positive and negative fold-changes), such that these genes fall at the very top and bottom of the rank-ordered list that GSEA is using to compute NES. So, do t…

gsea

updated 4.6 years ago • penny.lane

Is there any tool/package/test to perform GSEA-like analysis between two weighted ranked lists of unequal length? Essentially I want to test if genes which rank high...in one list also tend to rank high in the other list, but also consider the associated scores for each gene, not just its rank. Example scenario is to test...for over-representation of cluster-specific genes from single-cell exper…

RNA-Seq GSEA enrichment analysis microRNA R

updated 4.9 years ago • PeterA

GSEA results obtained using a 'pre-ranked' file (NO GMT file) - how do I run Enrichment Map in Cytoscape - in the absence of a GMT file

rna-seq

updated 4.1 years ago • claudia.santos

Can somehow GSEA tell me which gene set is most significantly enriched in our set of analysis. It gives ES, FDRp values. Alternatively, Is...there any tool that will give me a ranking of different pathways enriched in my list of genes

pathway

updated 4.1 years ago • kanwarjag

Hi All I am trying to run GSEA preranked on a ranked DEG list. I am choosing Wnt/bcatenin Hallmark gene subset database and keep getting the following...error message. Error Details ``` ---- Full Error Message ---- Error at index 0 in: "\pub\gsea\gene_sets\h.all.v7.1.symbols.gmt" ``` The error message doesn't come up when i use the gene matrix database (from website

RNA-Seq

updated 10 months ago • alaknandaadwal

Hi all, I am a bit confused with GSEA and I was hoping that you could help me. I've got RNA-Seq data (two conditions with 5 replicates each). The GSEA website says...that the suggested method is the standard one vs the pre-ranked so I decided to give it a try. I have read the following on [this][1] paper: "Gene set permutation is recommended for studies...five per condition). In this case, dif…

GSEA RNA-Seq

updated 4.2 years ago • pennakiza

Hi all, As per PANTHER manual, statistical enrichment test uses Mann-Whitney U Test (Wilcoxon Rank-Sum Test) to find enriched pathways. It requires a input file with two columns (gene id and expression values). It did not...Hi all, As per PANTHER manual, statistical enrichment test uses Mann-Whitney U Test (Wilcoxon Rank-Sum Test) to find enriched pathways. It requires a input file with two…

panther ranked-gene-list pathway-enrichment

updated 3.9 years ago • kousi31

to do this. I want to understand if enrichr performs enrichment using hypergeometric method or the GSEA (Kolmogorov-Smirnov test) method, in case of hypergeometric method is it possible to provide a list of background genes...and interesting/significant genes? Can enrichr handle a ranked list, rank could be anything like the t-statistic, fold-change etc? Thanks

pathway analysis genome RNA enrichr

updated 6.3 years ago • halo22

R to conduct RNA-seq analysis. After performing DESeq2 analysis, I executed the following code for GSEA analysis: res <- as.data.frame(counts(dds, normalized=TRUE)) res <- results(dds, contrast = c("condition", "exp", "cont")) res <- as.data.frame...in a file with columns for ID, Description, setSize, enrichmentScore, NES, pvalue, p.adjust, qvalue, rank, leading_edge…

GSEA

updated 10 weeks ago • 원진

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