Bioconductor Forum

div class="preformatted">Hello All , I have a list of genes (HUGO gene symbols ) or Entrez IDs . I would like to get the entrez gene summaries for those genes. Does any one know if there...is R package exits by which I get obtain entrez gene summary. e.g http://www.ncbi.nlm.nih.gov/gene/1 I would like to extract summary part from this page. Thanks Cheers

updated 13.5 years ago • Amit Kumar Kashyap

Bubba Gump wrote: > I have been hearing some news about the upcoming move from LocusLink > to Gene from the NCBI > (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene and a web > article). How will this transition be...the transition is finalized, we plan to provide updated meta data packages built against the new Entrez Gene database in a timely manner. These upda…

updated 20.9 years ago • Seth Falcon

Dear all, I want to find out on which Chromosome a Gene is. I am trying to adapt below code which uses the Gene Entrez to get the Chromosome Location. I already have my dataset d1...with one column containing the Gene Entrez, but I don't quite get below code adapted for that: ``` # select() interface: ## Objects in this package can be accessed using...AnnotationDbi package. See ?select for deta…

org.Hs.egCHR org.Hs.eg.db

updated 5.1 years ago • Bine

Hi all, I've finished up with an analysis and in reviewing some of the annotations for gene symbols and RefSeqs, I've found some discrepancies that I don't know how to explain. The discrepancies are between Affy...1.12.0" > mget("1558097_at", hgu133plus2LOCUSID) $`1558097_at` [1] 8971 On NetAffx, the Entrez Gene ID shows 253143. I've got about 12 other probe sets that BioC and Affy di…

Annotation GO probe affy Annotation GO probe affy

updated 19.7 years ago • Jacob Michaelson

div class="preformatted"> Dear list, Im struggling retrieving the full list of the entrez geneIDs for each of the enriched chromosome bands (obtained by "GOstats"). revmap(org.Hs.egCHR) doesnt give the entrezIDs...for the whole arm: mget(c("16", "1q"), revmap(org.Hs.egCHR), ifnotfound=NA) # Map between Entrez Gene IDs and Chromosomes $`1q` [1] NA revmap(org.Hs.egMAP…

updated 15.3 years ago • Xi Zhao

Rsubread R/Bioconductor package) and gencode annotation file to do features sumarization, but the gene ids are as below, how can i convert those  ID to entrez gene ids. \[1\] "ENSMUSG00000102693.1" "ENSMUSG00000064842.1" "ENSMUSG00000051951.5...the ids like this mart <- useMart(biomart = 'ensembl', dataset = 'mmusculus\_gene\_ensembl') genes$entrez <- select(x = mart, …

biomart rsubread gencode

updated 7.2 years ago • YinCY

div class="preformatted">Hi all, I am converting the HGNC symbols from an Illumina human array to Entrez ID using biomaRt. I found that there are some gene symbols are matched to many Entrez IDs, and vice versa. I am wondering...if how to solve the problem, so one gene symbol is only matched to one Entrez ID. Or is there any other package that I can use for matching gene symbols to Entrez...I…

biomaRt biomaRt

updated 14.3 years ago • Wendy Qiao

<div class="preformatted">Hello, I have been trying on the UCSC table browser to find a table that links kgIDs with gene IDs, but I did not find that. With the package GenomicFeatures, when constructing a TranscriptDB object from UCSC, one can...Hello, I have been trying on the UCSC table browser to find a table that links kgIDs with gene IDs, but I did not find that. With the package Gen…

TranscriptDb TranscriptDb

updated 14.9 years ago • Arnaud Amzallag, Ph.D

I've by now arrived to the end of my analysis, missing only the pathway analysis to contextualize genes with different expression levels. The workflow itself is studied for mouse genes, and suggests, at a point, to import Entrez...Gene Ids from the org.Mm.eg.db package (for mouse) as follows. library(org.Mm.eg.db) y$genes$Symbol <- mapIds(org.Mm.eg.db...annotation data. I on…

annotation entrez gene ids software error

updated 6.7 years ago • Raito92

easy to solve problem: I have RNA-seq data with Ensembl rownames and want to map them to symbol and entrez, because I need them for other packages in the one or other format. But there seems to be a disconnection of Ensembl and...Entrez in both biomart and org.hs.eg.db for some genes. For example, if I want to map the IGHM gene, which has the Ensembl ID ENSG00000211899...filter="ensembl_gene_id…

ensembl entrez biomart org.hs.eg.db

updated 7.1 years ago • bettina.budeus

Hello, I have a file of my differential expression output consisting of gene symbols that I want to convert to ENTREZ IDs. Is there a way to convert it in the original file and discard ones that don't...convert along with their corresponding data? E.g. the columns are gene name, basemean count, adjusted p-value and I want to convert all of the gene name column and discard any rows with improper..…

AnnotationDbi org.Mm.eg.db

updated 3.8 years ago • rl19

I need to map mouse Ensembl gene ID's to their corresponding Entrez Gene ID's. In the process of reviewing cases of multi-mapping ID's, I came across a few examples...where the wrong Entrez ID is assigned to a corresponding Ensembl ID. For Example: ![Mismatch for Zinc Finger genes][1] Are all recognized by NCBI...and in most cases the NCBI gene page recognizes the correct Ensembl annotation:…

org.Mm.eg.db AnnotationDbi

updated 4.4 years ago • abf

div class="preformatted">Hello all, Is there anyway to retrieve the gene symbols, full names (discription), or other gene information, given a list of Entrez Gene IDs (or the LocusLink) in Bioconductor...Obviously, one way is to query Entrez Gene web service ID by ID, but is there any way to get connected to that web service from within R/Bioconductor and retrieve...the specific fields only( l…

Annotation Annotation

updated 19.5 years ago • Luo Weijun

div class="preformatted">I have been hearing some news about the upcoming move from LocusLink to Gene from the NCBI (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene and a web article). How will this transition be handled

affy affy

updated 20.9 years ago • Bubba Gump

div class="preformatted">Hi everyone, Is there a way to map an Entrez ID to a gene symbol using the bioconductor annotations? I would've expected that to be in the xxxLLMappings annotations...not. I'm matching a couple of lists from different sources (including custom cDNA). Human-readable gene symbols make it a lot easier to deal with those lists. There are a couple of other ways of doing …

biomaRt biomaRt

updated 19.2 years ago • Francois Pepin

Is there a way to get latest gene Symbol or Entrez ID in R? I am using `AnnotationDbi` and org.Hs.eg.db but it seems to give old gene name. For entrez ID 64755...the new gene name is [RUSF1][1] but it gives C16orf58 ```r library(AnnotationDbi) library(org.Hs.eg.db) AnnotationDbi::select(org.Hs.eg.db...pkgconfig_2.0.3 [13] memoise_2.0.0 ``` [1]: https://www.genecards.org/cgi-bin/carddisp.pl…

AnnotationDbi org.Hs.eg.db

updated 4.8 years ago • sgupt46

Hi, I have a microarray data that I would like to do GO analysis using GOSeq. However, I have ENTREZ gene ids. When I am trying to convert ENTREZ ids to ENSEMBL ids, I lose several of my genes from the universe, either because...of 1:many mappings or no ENSEMBL ids. Is there a way to to use ENTREZ ids as names of the gene universe? The data frame has also ENSEMBL transcript ids, Gene Name, REFS…

goseq entrez gene identifiers

updated 9.7 years ago • Mehmet Ilyas Cosacak

Below, GG is the list of gene symbols to be mapped into entrez. The code is: geneMapping2= select(org.Hs.eg.db, GG, c("ENTREZID","GENENAME"),"ALIAS") The error...Below, GG is the list of gene symbols to be mapped into entrez. The code is: geneMapping2= select(org.Hs.eg.db, GG, c("ENTREZID","GENENAME"),"ALIAS") The error is: Error in .testForValidKeys(x, keys, keyt…

limma annotation Gene

updated 5.9 years ago • omarrafiqued

<div class="preformatted">Hi, I have a batch of genomic coordinates, and I need to find all the genes (Entrez Gene ID) covered by those coordinates. I am new to R, but I am able to use biomaRt in R to get various annotation of genes from gene ID lists. Would it be possible to retrieve my IDs from the coordinates? The coordinates are in the chr:start:end format; I...div class="preformatted"…

biomaRt biomaRt

updated 12.1 years ago • Bruna Marini

Now I click a link, the locuslink page tells me its closed and that I'll be redirected to Gene. I've looked at the code and it referred to a function getQueryLink(). this last function does not have an entry for Entrez...Gene. Has anyone else dealt with this problem? Thanks for your assistance. Ramsi -- Ramsi Haddad, Ph.D. Functional Genomics Laboratory

updated 20.8 years ago • Ramsi Haddad

I want to replace the index of the dataframe (Gene Symbols) with `GENE_ID:GENE_VALUE` to use as a data matrix input for netgsa R package (https://cran.r-project.org/web/packages...netgsa/vignettes/netgsa.html). First, I retrieve the Entrez IDs: library(org.Hs.eg.db) library(AnnotationDbi) # gene_value is the Entrez ID gene_value = mapIds(org.Hs.eg.db, keys

AnnotationDbi

updated 3.4 years ago • Melissa

div class="preformatted">Hi, I wanted a table that provides a mapping from Entrez Ids to Gene Symbols for homo sapiens. To do this, I used the following code: ---------------------------------------------------------------------- -------------------------------------------- library(org.Hs.eg.db) x <- org.Hs.egSYMBOL...Get the gene symbol that are mapped to an entrez gene identifi…

Cancer Homo sapiens convert Cancer Homo sapiens convert

updated 16.9 years ago • Tim Smith

Hi all, I am using the GSVA package for some analysis. I found that the package only takes the gene expression matrix annotated with affymetrix probe IDs, although the gene set collection is made of Entrez IDs. I imagine...there a step in the package for converting the Affymetrix probe IDs to Entrez IDs. As my data are from the Illumina platform, I am wondering if an expression matrix annotated …

probe GSVA probe GSVA

updated 14.2 years ago • Wendy Qiao

it a central ID for the org package you name for it. It seems to be assuming that this will be an entrez gene ID. But that is *not* what the arabidopsis community usually uses. That community likes to use TAIR IDs. So the org.At.tair.db...IDs as the central ID (this is why TAIR is in the middle of the package name). You can get and use entrez gene IDs with the org.At.tair.db package, but the…

GO Organism goProfiles GO Organism goProfiles

updated 12.4 years ago • Marc Carlson

It seems to me that using `annotate::lookUp` used to work for mapping ENSEMBL genes to ENTREZ IDs. I used to use it in the following way: > annotate::lookUp("ENSG00000121410", data = "org.Hs.eg", what = "ENSEMBL") However...ENSG00000171428 5 10 ENSG00000156006 6 12 ENSG00000196136 ``` Take the first ENSEMBL gene from `temp` to use with `annotate::lookUp` (it should re…

annotation

updated 6.7 years ago • Vitalina Komashko

Hi all, I was using goProfiles package for functional analysis using a genelist of 316 Arabidopsis entrez gene IDs as shown below in the R command sessionInfo(). - Read a file containing Entrez IDs and TAIR IDs. - Subset the Entrez...1] "839235" "838362" "838961" "837091" "837455" "837543" > >> h<-basicProfile(b,idType="Entrez",onto ="ANY",level=2,orgPackage="org.At.t…

goProfiles goProfiles

updated 12.4 years ago • Guest User

div class="preformatted">Hello All I am using GSE4137 for identifying differentaily gene expression analysis. For annotation i am using the platform annotation file provided by the vendor alongside their...microarray platform. It has the GB_ACC number for each probe id. I want the corresponding entrez ids for each GB_ACC. My query is :- *How to convert GB_ACC number into Entrez id using R an…

Microarray Annotation probe convert Microarray Annotation probe convert

updated 14.0 years ago • Reema Singh

know if there is any package (perhaps biomaRt) that I can use for me to convert IMAGE Clone ID?s to Entrez Gene ID?s. Kind regards, Jo?o Fadista </div

convert convert

updated 18.7 years ago • João Fadista

of proteins derived from MS. I am given IPIs by the proteomics folks and need the corresponding Entrez Gene IDs. Putting aside the issues of non-unique mapping from IPI to EG, isoforms, etc., I was wondering if anyone would comment...on my method of getting the Entrez Gene IDs. I'd really like to use Marc Carlson's merge method (shown below), but that approach seems to miss several thousand...2…

Proteomics GO biomaRt Proteomics GO biomaRt

updated 14.8 years ago • Dick Beyer

What is the best way to convert uniprot accessions to entrez gene identifiers? What is the best way to reverse the map org.Hs.eg.db::org.Hs.egUNIPROT ? Is there any better approach

org.hs.eg.db uniprot accessions entrez gene identifiers

updated 10.4 years ago • Aditya

Hi, I was using the hyperGTest in GOstats to find significant KEGG and PFAM terms. I have the entrez IDs of a set of genes and I test these with a universe of entrez IDs in hyperGTest to get the significant KEGG and PFAM...terms. Now, I want to know which particular entrez IDs in my set of genes map to a particular significant KEGG/PFAM ID. I checked the KEGG.db (and PFAM.db) packages, but they…

GOstats GOstats

updated 17.2 years ago • Tim Smith

the HG-U133A and, as an initial step after creating an rmaset, I filter out the probesets without Entrez gene IDs as follows: arrayset <- ReadAffy() rmaset <- rma(arrayset) entrezIds <- mget(featureNames(rmaset), envir = hgu133aENTREZID...However, when I manually scanned the annotated table I discovered a number of probesets with an Entrez ID but no other annotation. Most of…

Annotation hgu133a limma Annotation hgu133a limma

updated 17.6 years ago • David Fermin

I'm not very experienced with bioconductor and R, and I am struggling with converting a list of gene symbols I've read in from a .csv file into R into their relevant ENTREZ ID(s). I was wondering if anyone had any tips for how to

org.hs.eg.db entrez gene identifiers genesymbols

updated 7.9 years ago • imalumberjack

Hi, For my study, I have to convert gene symbols to Entrez IDs. So, by using "org.Dr.eg.db" package and  my annotation file(annot) I wrote below code: <pre> library

org.Dr.eg.db Entrez ID

updated 7.2 years ago • modarzi

div class="preformatted">Dear List, could anybody help on how to insert columns in TopTable for entrez gene id, gene name and symbol when using the hugene1.0ST arrays. When using the regular 3'IVT arrays such as the hgu133plus2...I used the following lines without a problem > *ebayes$genes$Symbol=getSYMBOL(ebayes$genes$ID, "hgu133plus2")* > *ebayes$genes$EG <- getEG(eb…

hgu133plus2 hgu133plus2

updated 15.1 years ago • Marcos Pinho

analysis using ClusterProfiler. However, I'm facing a problem that I'm unable to convert the ENSEMBL gene names to ENTREZ ID. Can you please help me with that? Below all information about the code and Error I'm getting. Code should...library("org.Mm.eg.db") >sigs.df<- as.data.frame (df3) >sigs.df X Gene pvalue log2FoldChange pct.1 pc…

clusterProfiler

updated 3.5 years ago • martacrespi7

div class="preformatted">Hey I am looking for genome locations for a list of entrez ids. I have used org.Hs.db in the past. However there are several ids in my list which do not have annotation in the database

Annotation Annotation

updated 15.4 years ago • Bhatti, Gaurav

normalized and summarized expression values for affymetrix probesets, av.data. I have looked up the Entrez gene ids for the probesets in the annotation package, entrezids. Multiple probesets map of course to the same entrez...and I would like to combine these data into one row, by averaging the expression values for the same entrez ids over the different experiments. I tried the function "aggrega…

updated 17.2 years ago • Vanessa Vermeirssen

error while trying to select a particular SYMBOL using a GENEID using the Homo.sapiens package. The Entrez ID '6218' maps to the Gene Symbol 'RPS17'. When I try to use the select interface to retrieve the gene symbol for only the above...entrez id I get an error but if I combine the id with a couple of other entrez ids it works. Here is a reproducible example: <pre> select

homo sapiens

updated 10.8 years ago • Moiz Bootwalla

Hello! I'm trying to convert a set of 6422 gene symbols into EntrezID's (I got this list of genes from doing a differential expression analysis with TCGAbiolinks on...of hepatocellular carcinoma) and I'm trying to use AnnotationDbi for that. When I do this, 838 genes return an NA for ENTREZID. However, some of them do have an Entrez ID associated with the name that was provided in the original..…

AnnotationDbi org.Hs.eg.db

updated 5.1 years ago • Emilia

15 AM, varpal singh <gilvarpal@gmail.com> wrote: > Hi Sir,, > > I would like to know about entrez id of arabidopsis, I have probe ids of > differential expressed genes, I wan to know about their entrez id by > bioconductor

updated 15.7 years ago • Sean Davis

analysis. I have used the edgeR package to get the differentially expressed. I am able to add the ENTREZ ID as a new column. However, I want to change the rownames of "degs" from ENSEMBL to ENTREZ ID, instead of adding it to a new...pheno$Sample) dge<- calcNormFactors(dge) cpm<- cpm(dge, log=T) # Filtering low count genes keep<- filterByExpr(dge) dge<- dge[keep,…

AnnotationData

updated 3.8 years ago • Manav

appreciate it very much if you could give me some help. I got a list of differential expressed genes from microarray analysis by using limma. Then I did GO enrichment analysis on these genes by hypeGTest() method available...in GOstats package. Now I want to retrieve entrez gene IDs in my gene list that correspond to each enriched GO terms. I found there are two ways to get the entrez gene IDs..…

Microarray Annotation GO limma GOstats biomaRt Microarray Annotation GO limma GOstats

updated 16.3 years ago • Yuan Hao

div class="preformatted">I have an expression set where the featureNames are already human entrez ids. What annotation package should I use to run GSVA? I tried org.Hs.eg.db, but I get this error: > coad_es<-gsva(entrezSet...c2BroadSets, min.sz=10, max.sz=500, verbose=TRUE)$es.obs Mapping identifiers between gene sets and feature names Error in GeneSetCollection(lapply(what, m…

Annotation Annotation

updated 13.9 years ago • Ed Siefker

such as AnnotationDbi or the organism packages. For example I wonder if there is a way to convert an Entrez Id to convert gene Entrez to symbols and other IDs using AnnotationHub, or if I still have to rely on AnnotationDbi and...packages. In general I have a bit of confusion regarding which is the correct way to convert gene id from one type to another in bioconductor, without using biomaRt. Can…

conversion symbol entrez

updated 10.3 years ago • dalloliogm

in enrichment analysis. However, there is a problem confusing me in ID transformation. I have a gene list containing 39570 genes with ensembl ID. 1. After transformation with bitr function from Ensembl to entrez ID, the...number of genes is 22142, 44.39% of input gene IDs fail     to map. 2. Transformation with bitr function from Ensembl to Symbol...nbsp;the number o…

clusterprofiler

updated 7.1 years ago • tenger929

code/directions to get it working... Thanks, Guido   I have a data frame consisting of human Entrez IDs, which I would like to convert into Gene Symbols. NAs should preferably be removed. How to best do this? the `` select() `` function

annotation

updated 9.0 years ago • Guido Hooiveld

Hello everyone, I have a vector of 2906 ensembl transcript ids and I want to find their entrez gene ids using biomart, so I can do pathway analysis with gage. The problem is that using the code below, I only obtain&nbsp

biomart ensembl ensemble mart entrez gene identifiers

updated 9.9 years ago • serpalma.v

<div class="preformatted">After my premature posting yesterday, I am bit hesitant to ask, but I am puzzled by what I am getting from biomaRt. (To avoid clutter, I added the sessionInfo at the end of the message.) I used ReadAffy() to read in a rat dataset and called it CELdata. CELdata AffyBatch object size of arrays=834x834 features (19 kb) cdf=Rat230_2 (31099 affyids) number of samples…

biomaRt biomaRt

updated 11.8 years ago • Naomi Altman

to get the releveant set of genes. Currently, what I'm doing is finding the significant GO terms by using the following code: ----------------------- ### 'genes1' are the Entrez IDs of...my genes of interest, and 'allGenes' is the universe of Entrez IDs paramsGO <- new("GOHyperGParams", geneIds = genes1, universeGeneIds...This gives me a set of significant GO terms. Now, I wo…

Annotation GO Annotation GO

updated 17.2 years ago • Tim Smith

figure out how to take some CEL files from an Affy U133A chip, RMA them, and combine probesets into entrez IDs. I've tried searching the bioconductor help lists but can't find an appropriate thread, though I'm sure this has been

affy affy

updated 14.9 years ago • Brian Tsai

Hi all, I've been following the RNAseqGene vignette and am having trouble adding annotations for Gene Ontology using the org.Mm.eg.db. Adding gene symbols and Entrez id's worked fine but nearly all GO id's return as NA...whether I used the ensembl ID's or entrez ID's as the database key. Thanks for the help. Michael convertIDs <- function( ids, from, to, db, ifMultiple=c("putN…

org.mm.eg.db annotation rnaseqgene

updated 10.5 years ago • michael.willcockson

GOstats and Kegg.db for over representation and pathway analysis. When converting my Ensembl gene IDs to Entrez IDs (required by the GOstats) using the annotation package, I found that 398 of my genes were not assigned to...any Entrez ID and 457 were assigned to more than one Entrez ID (sometimes 5 different Entrez IDs). When I checked for the genes with...more than one Entrez IDs, I found that m…

rnaseq annotation gostats org.Bt.eg.db

updated 9.8 years ago • mrodrigues.fernanda

name of a probe set from an Affymetrix platform (doesn't matter which one) corresponding to a given ENTREZ gene ID? It seems that it is fairly simple to obtain the entrez ID if you have a probe set, but the reverse problem seems...This gives me a set of significant GO terms. Now, I would like to find which subset of genes in 'genes1' is associated with each of the significant GO term. To do this…

aCGH Sequencing miRNA Microarray Annotation Normalization GO Preprocessing Visualization

updated 17.2 years ago • McGee, Monnie

div class="preformatted">Dear List, I want to extract ensembl gene ids from biomart to add to my microarray analysis output. However, there are some discrepancies that have me confused...regarding the entrez gene id and ensemble gene id. Array used: Illumina HumanHT12 v4. As an example: GAGE12F, GAGE12G, GAGE12I genes Microarray

biomaRt biomaRt

updated 14.4 years ago • Natasha

Hi, I'd like to use annotationDbi to map various gene IDs (entrez,ensembl, etc) to official gene symbols quickly, but some of the gene symbols in the org.Mm.eg.db database aren...t the official MGI gene symbols.  For example, mt-Cytb (entrez \# 17711) has the gene symbol CYTB according to org.Mm.eg.db. Am I using an inappropriate

org.mm.eg.db annotationdbi

updated 7.4 years ago • brendan.innes

a limma linear model analysis using expression data produced from affymetrix 1.1 st zebrafish gene arrays.  I am filtering differentially expressed genes between three contrasts and when I call the topTable function...p>ENSDART00000129395</p> </td> <td> <p>uvrag</p> </td> <td> <p>UV radiation resistance associated gene</p> </td&…

oligo

updated 9.1 years ago • mat149

div class="preformatted">Hi, Does anybody know how to obtain KEGG gene-ids for a list of affymetrix probesets. I manage to retrieve probesets or entrez-gene-ids for a given KEGG pathway, but I...need to know which probeset represent the individual KEGG gene (eg.: the gene "mmu:108960" is part of pathway "mmu04210", but what is the underlying entrez gene or probeset...) Thanks in advance

updated 20.2 years ago • Dr.Mayhaus Manuel

results <- hyperGTest(params) Error in getUniverseHelper(probes, datPkg, entrezIds) : No Entrez Gene ids left in universe Thanks, Ben -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: universe.txt

GOstats GOstats

updated 16.4 years ago • Benoit Ballester

I'm having issues resolving NAs whilst trying to annotate a list of diff genes with entrez IDs using ensembl IDs. I would be surprised if this hadn't been asked before, but finding answers and suggestions...is Homo_sapiens.GRCh38.v100 - I combined both coding and non-coding. I have list of diff genes for several compound-treatment experiments. I need entrez IDs for a chemistry process downstream…

annotation rna

updated 5.2 years ago • anthony.nash