Tag: enrichGO

cluster analysis – The enrichWP function is no longer recognized in `comparecluster()` (clusterProfiler R package)

I have been using clusterProfiler for quite a while, specifically the compareCluster() function. I have used enrichKEGG()and enrichWP()for my workflow since January 2023. But now fun = “enrichWP” isn’t recognized in the comparecluster() function. Indeed when checking the R doc, it does now state for the fun argument : One…

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Enrichment dotplot color

Enrichment dotplot color 0 Hi, I have a question about enrichGO or enrichKEGG dotplot. The dotplot I drew when using enrichGO() or enrichKEGG() was this color: But when I repainted it today it turned into this color: And I can’t change it back, can anyone help me get it back…

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KCouper/Liverpool K-means RNAseq Analysis November 2020

R3 VAR14 vs RBC no TNF k-means q0.05 1. Genelist Selection groupsName<-“R3_VAR14_kmeans_q0.05” countsTable<-read.delim(“RNAseq2019July_5.txt”, header = TRUE, sep = “\t”,check.names=FALSE,row.names=1) head(countsTable) AllGeneNames<-countsTable$Gene_Symbol #head(AllGeneNames) tempA<-countsTable topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_0h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_0h))####find indexes listA<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_2h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_2h))####find indexes listB<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_6h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_6h))####find indexes listC<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_20h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_20h))####find indexes listD<-tempA[ topDEgenes,…

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gene set enrichment analysis- by enrichGO

gene set enrichment analysis- by enrichGO 1 Hey, I ran DESeq and identified differentially expressed genes. I noticed that for running enrichment analysis, it’s recommended to select genes with a fold change bigger than 2. My question is, do I also need to filter by p-value or p-adj? Is this…

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A Bioconductor workflow for processing, evaluating,…

Introduction Proteins are responsible for carrying out a multitude of biological tasks, implementing cellular functionality and determining phenotype. Mass spectrometry (MS)-based expression proteomics allows protein abundance to be quantified and compared between samples. In turn, differential protein abundance can be used to explore how biological systems respond to a perturbation….

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Over Representation analysis altered pathways in common between comparisons plot

Hi! I did over representation analysis for the comparison group 1 vs group 2, group 1 vs group3 and group 2 vs group 3. I would like to plot an “upsetplot” style plot that has altered pathways for each subgroup has rows and has rows the comparions (e.g group 1…

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Which function is best for pathway analysis?

Which function is best for pathway analysis? 1 Hi Biostars, I found there are many function to perform pathway analysis such as fgsea(), gseGO(), gseKEGG(), enrichGO() which made me quite confuse which result I should focus on. Getting a correct background gene set is important. However, how can we find…

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Deseq2, enrichGO and ensembl ID

Deseq2, enrichGO and ensembl ID 1 @3cc02754 Last seen 5 hours ago United Kingdom Hi I used code initially in DESEQ2 dds=DESeqDataSet(se,design=~TRAIT) dds=DESeq(dds) res=results(dds) I currently have results from DESEq2 which looks like this: log2 fold change (MLE): TRAIT S vs N Wald test p-value: TRAIT S vs N DataFrame…

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r – DEseq2 results, enrichGO and ENSEMBL ID not matching

I am trying to do DEG and then use enrichGO on the results. I used code initially in DESEQ2 dds=DESeqDataSet(se,design=~TRAIT) dds=DESeq(dds) res=results(dds) I currently have results from DESEq2 which looks like this: log2 fold change (MLE): TRAIT S vs N Wald test p-value: TRAIT S vs N DataFrame with 42800…

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Gene Ontology – How to do Transcript Ontology?

Gene Ontology – How to do Transcript Ontology? 0 Hi all, I am very new and I apologize if I ask very basic and stupid questions. I’ve been kind of thrown into doing transcriptomics and there isn’t anyone in my lab who can teach/help me with this. I have run…

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Ensembl site unresponsive in clusterProfiler analyses

Ensembl site unresponsive in clusterProfiler analyses 0 Hi, thanks for all the useful work. I’m writing to ask about an issue I’ve recently encountered with clusterProfiler in its latest version. I’m trying to implement an approach using parallel::mclapply and some clusterProfiler functions (e.g. groupGO, enrichGO, gseGO) to process few sets…

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Load MF, CC and BP from org.Hs.eg.db

Hi! I would like to load all the pathways related to CC, MF and BP from the org.Hs.eg.db, converting into a dataset that has as columns pathway, gene_symbols. In order that after this I filter the pathways that have genes in common with the metabolism pathways from KEGG. So that…

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Over Representation Analysis over one specific pathway

Over Representation Analysis over one specific pathway 0 Hi! Let’s say I would like to analyse if a particular pathway is enriched how would I do that given that I have a set of DGE genes resulting from 1500 genes of RNA Seq? I do not want to analise any…

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Enricher with Gene Symbols

Enricher with Gene Symbols 0 Hi! I have a list of genes with abs(logfc) >= 0.9 like this: > genes [1] “MDM2” “CDK4” “CCND2” “FLNA” “RBP7” “EDNRB” “EPHA4” “PTPRB” “PPP1R13L” “TPM1” “INSR” [12] “DLC1” “WNT7B” “SFRP1” “IFI16” “ZMAT3” “MEST” “AKT3” “CD36” “SRD5A1” “KIF23” “EPOR” So the list has the gene…

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gseGO() –> No gene can be mapped

Dear all, I have a list of S. cerevisiae genes and I want to do GO enrichment analysis using clusterProfiler. I already obtained some information using enrichGO() and groupGO(), and I want to see what I can obtain with gseGO(). I use the package org.Sc.sgd.db as my organism database. Here…

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Does the gene universe for enrichGo need to be a list of gene names?

Does the gene universe for enrichGo need to be a list of gene names? 1 Hello, When using the enrichGo does the gene universe need to be a gene list or can it be a named list with logfc? Currently I am doing this: genes <- names(gene_list)[abs(gene_list)> 0.9] go_enrich <-…

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Optimal Over Representation Analysis DE genes foldFC threshold?

Optimal Over Representation Analysis DE genes foldFC threshold? 0 Regarding Over Representation analysis over identification of DGE genes, firstly I have a set of 1550 genes resulting of RNA Seq. Given this number decided to do ORA instead of GSEA. After choosing ORA, I have to pass to enrichGO a…

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Extract geneID following GO enrichment analysis

Hello, I have performed GO analysis using enrichGO function provided from Clusterprofiler package used in R. This is my code I used for that as follows: ego = enrichGO(gene = df$REFSEQ, OrgDb = “org.At.tair.db”, keyType = “TAIR”, ont = “ALL”, pAdjustMethod = “BH”, pvalueCutoff = 0.05, qvalueCutoff = 0.05, readable…

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How to extract genes of a specific GO-term/pathway

clusterprofiler: How to extract genes of a specific GO-term/pathway 2 I was wondering how to get the list of genes grouped in a particular GO-Term of Biological Pathway. I have an enrichGO output (using the clusterprofiler package). From this result, I’ve into a bar plot (see below). For example, my…

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Epigenetic dysregulation from chromosomal transit in micronuclei

Cell culture Cell lines (MDA-MB-231, 4T1 and RPE-1) were purchased from the American Type Culture Collection (ATCC). TP53-knockout MCF10A, TP53-knockout RPE-1 and Trex1 knockout 4T1 cells were gifts from the Maciejowski laboratory at the Memorial Sloan Kettering Cancer Center (MSKCC). OVCAR-3 cells were a gift from J. D. Gonzales. All…

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clusterprofile enrichment analysis

clusterprofile enrichment analysis 1 Hello, Can I use clusterprofile enrichment functions like enrichGO() in case I have ensemblId and symbol(gene name) from old version GTF file (as they will not mapped or join with org.Hs.eg.db ). and which database can be passed for OrgDb param in enrich GO other that…

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Performing GO analysis from Differential Peaks

Performing GO analysis from Differential Peaks 0 Hello everyone, I called for FindMarkers() in order to find differential peaks between two biological conditions and the following was output (“diff.peaks”). My question is how would I generate a nice chart for GO analysis from this? My current code is: install.packages(“JASPAR2022”) library(JASPAR2022)…

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Problems with the input (from TPM) to run the WGCNA

Hello everyone, Initially I express that I am not very expert in bioinformatics analysis. I have the TMP from RNAseq data. These data come from Arabidopsis seeds infected with a fungal inoculum. I select the data by calculating the zscore. Thanks to the tutorials and the forums I have managed…

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Questions about DESeq and GOenrichment analysis for tomato

Questions about DESeq and GOenrichment analysis for tomato 0 Hello all, I am a beginner for bioinformatics and I have 2 questions about RNAseq data processing for tomato. 1) I am always confused about the DESeq’s normalization function for gene length. I have 2 data sets at hand, one is…

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How to plot the result of compareCluster using ggplot

Hello, I am trying to plot the result of compareCluster. ck = compareCluster(geneCluster = data, fun = enrichGO, OrgDb = “org.At.tair.db”, keyType = “TAIR”, ont = “BP”, pAdjustMethod = “BH”, pvalueCutoff = 0.05, qvalueCutoff = 0.05, readable = TRUE) After this code, I get the result, but there is another…

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different package different padjusted and qvalue

Hi! Apologies for the stupid question! but I think I am doing something wrong but i do not understand what. I would like to do ORA analysis on bulk-RNAseq dataset so I tried both clusterProfiler and also genekitr.` However, despite getting the same terms, but I have different p-adjusted value…

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Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?

In several manuals (example) on ChIP-seq analysis they pre-select, for instance +1000bp and -1000bp from the TSS as the “promoter-bound” regions: peakAnno_bcl11b <- ChIPseeker::annotatePeak(peak = ‘bcl11b_peaks.narrowPeak’, TxDb=txdb, tssRegion=c(-1000, 1000) ) which produces an object with a slot @anno in which each peak is assigned either “Promoter”, “5’ UTR”, “3’ UTR”,…

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Error when using compareCluster from enichment

Error when using compareCluster from enichment 0 I have two data frames of RNA translated to the Entrezid Ids and when running the chunks through compare cluster I get the following error: Error in $<-.data.frame(*tmp*, “Cluster”, value = integer(0)) : replacement has 0 rows, data has 120 The data is…

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How does enrichGO function calculated p-value?

Hi, I’m doing an Over Representation Analysis using the clusterProfiler package. When I used the enrichGO function, I obtained a dataframe with the following columns: _ONTOLOGY: BP (in my case) _ID: GO ID. _Description: Description of the Biological Process. _GeneRatio: ratio of input genes that are annotated in a term….

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Error in UseMethod(“rescale”)

Error in UseMethod(“rescale”) 0 @2528ae94 Last seen 17 hours ago United States While using cnetplot to plot enrichGo results, I am getting the following error. It used to work before, but now I am constantly getting this error. I am using clusterprofiler package gse <- enrichGO(gene = deGenes, ont =…

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Cnet plot showing non-significant genes within pathway

Hi All, I am trying to make cnet plots of differentially expressed genes between 2 tissue types, looking at specific pathways identified from enrichGO analysis. When I plot this a bunch of non-significantly regulated genes are appearing as uncolored dots and I am not sure how to stop this from…

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Cluster Profiler output not the same as Enrichr output

Cluster Profiler output not the same as Enrichr output 0 @angkoo-23537 Last seen 18 hours ago United Kingdom Hi there, I have am getting different outputs after running enrichGO on cluster profiler when I put the same genes into enrichR (by Maayan Lab) website. Example here using Biological Process 2021…

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How to transform the deg gene list from seurat to a gene list input to clusterProfiler compareCluster ?

Sorry for lateness, I wanted to do something similar. This is what I did for reference: Using a Seurat generated gene list for input into ClusterProfiler to see the GO or KEGG terms per cluster. I’ll keep the meat and potatoes of the Seurat vignette in this tutorial: library(dplyr) library(Seurat)…

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FindMarkers for ClusterProfiler

FindMarkers for ClusterProfiler 1 Hi, I recently ran FindMarkers to compare DEG between two different clusters in a single-cell RNA-seq analysis This is my code: markers= FindMarkers(obj, ident.1=c(4), ident.2 = c(5)) head(markers) dim(markers) table(markers$avg_log2FC > 0) table(markers4v5$p_val_adj < 0.05 & markers$avg_log2FC > 0) I would like to run ClusterProfiler to…

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