Tag: entrezID

Dot Plot using KEGG 2 Hi, I´m trying to do a dotplot using data from KEGG. I have my data represented, but I don´t want the species name in the X axis. My comand is: kegg_gene_list = sort(kegg_gene_list, decreasing = TRUE) kegg_gene_list = sort(kegg_gene_list, decreasing = TRUE) kegg_organism = “mmu”…

Converting RefSeq protein accession IDs into entreZ IDs 0 Hi, I have a list of genes with Refseq accession ids and I want to convert it to EntrezID, which can then be fit in the GENE ONTOLOGY enrichment and pathway analysis like DAVID and gProfile (these IDs belong to a…

bitr() doesn’t recognize the keys I’ve entered as valid gene symbols for my organism’s database (‘SYMBOL’). 0 Hello, In trying to re-run my pathway analysis with a DEG set annotated with gene symbols. I have encountered this error while wanting to retrieve Entrez IDs for clusterProfiler. This is a new…

A large portion of gene ID cannot be mapped when running the “bitr” command of the “clusterProfiler” package 0 Hello everyone, When I run the bitr command, I get warning message saying that 58.9% of input gene IDs are fail to map…, like the following: library(ggplot2) library(clusterProfiler) > gs.up =…

Error in change Affymetrix transcript cluster id to Gene Symbol in microarray 0 annotLookup <- select(hugene20sttranscriptcluster.db, keys = “TC1000011370.hg.1” , keytype = “ENTREZID”, columns = c( “ENSEMBL”, “SYMBOL”, “ENTREZID”)) Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for ‘ENTREZID’. Please use the keys…

Hey, There are two approaches here. 1, org.At.tair.db You can use the annotation DB packages from Bioconductor, specifically org.At.tair.db. Copying my own answer from here: A: Biomart query returns NA when searching for entrez_id, while manual search works library(org.At.tair.db) genes <- c(“AT2G14610″,”AT4G23700″,”AT3G26830”, “AT3G15950″,”AT3G54830″,”AT5G24105”) keytypes(org.At.tair.db) mapIds(org.At.tair.db, keys = genes, column =…

data file link: drive.google.com/file/d/1Odr12yDiUwI02-BfaXrHehKBM1uMW_1N/view?usp=share_link Step 1 (5pts) Load the file GSE124548.raw.txt into R and create a new dataframe with just the columns with the raw counts for healthy (HC) and CF patients before treatment (Base) and call it readcount. Use the first column (EntrezID) in the original file as the…

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”,…

KEGG enrichment in R and gene IDs 2 @239caad3 Last seen 3 days ago Belgium Hi, I am trying to run a KEGG enrichment analysis on my data. My genes are in SYMBOL, which I converted to ENTREZID, but I need them in “kegg” or “ncbi-geneID” to run enrichKEGG. I…

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…

Hello There! I am doing the enrichment analysis based on kegg. The analysis is based on zebrafish entrezid/ncbi-geneid Clusterprofiler seems to work for this example. data(geneList, package=”DOSE”) de <- names(geneList)[1:100] yy <- enrichKEGG(de, pvalueCutoff=0.01) head(yy) But when I tried my code, it does not work. I did it for my…

gseKEGG – no gene can be mapped (RNAseq analysis) 0 Hi all, I have been trying to extract the GSEA results from a list of genes after RNAseq analysis. It looks like my gseKEGG function is giving me problems. I am unable to generate a list of KEGG terms, it…

Dear Community, I am trying to show pathway expression in 6 clusters that I identified in disease and control and would like to compare the corresponding clusters. I followed this post 438466 and used Pratik ‘s solution. Which gives me a plot only for the disease. However, I would like…

There is no way to specify the source of gene symbols for an OrgDb. For TEC, one comes from HGNC, and the other comes from OMIM. When we generate the OrgDb packages, we don’t distinguish between sources, as they are all (as far as NCBI is concerned) ‘real’ gene symbols….

I’m trying to annotate some data from a Bisulphite experiment, from which I have a GRanges object without any annotation: GRanges object with 872900 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr10 48196 * [2] chr10 48486 * [3] chr10 49247 * [4] chr10 49258…

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…

Hi, I would use the pre-built Bioconductor annotation databases / packages for this array (I have used this array a few times over the years): mogene10sttranscriptcluster.db mogene10stprobeset.db Most likely mogene10sttranscriptcluster.db is what you want: require(mogene10sttranscriptcluster.db) columns(mogene10sttranscriptcluster.db) [6] “ENTREZID” “ENZYME” “EVIDENCE” “EVIDENCEALL” “GENENAME” [11] “GO” “GOALL” “IPI” “MGI” “ONTOLOGY” [16] “ONTOLOGYALL”…

What to do if the Entrez id that I have had been updated with a new one and now is associated with a gene 0 For context, this is part of an RNAseq analysis, I have a list of genes, which was generated by annotateMyIDs using the Entrez id from…

My data is a file of about 19000 genes from a 100 patients. I tried to use these data to create a network by using igraph. Firstly, I had all the names of the genes converted to ENTREZID and from the 19000 genes I kept around 14000. Then I had…

GO Enrichment Analysis in R – Count all the parents of each Term 0 Hi, I’m trying to implement a new GO tool in R. After I have a list of genes, I’m using the following code to retrieve the relevant annotation for each gene: library(AnnotationDbi) AnnotationDbi::select(org.Hs.eg.db, keys = genes.list,…

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)…

[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], hugene10sttranscriptcluster.db, AnnotationDbi 1 Hello, I have microarray data from the chip [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], and I am trying to annotate the probe IDs in R using the hugene10sttranscriptcluster.db package and the following function:…

I have a cnetplot from running enrichment with kegg using clusterprofiler. I have scores input as the fold change but for each gene in the plot they are not varying in colour to show their difference in the fold change score. My dataset is genes of entrez IDs and then…