Bioconductor Forum

UCSC.hg19<- TxDb.Hsapiens.UCSC.hg19.knownGene hg19.genes<- genes(UCSC.hg19) library("org.Hs.eg.db") gene_symbol<- AnnotationDbi::select(org.Hs.eg.db, keys=hg19.genes$gene_id, columns...I then went to IGV to check "LOC286297", the end coordinate is 42859085 The reason I found this gene is because I want to check how many genes in…

txdb.hsapiens.ucsc.hg19.knowngene

updated 9.2 years ago • tangming2005

div class="preformatted">I have access to gene sets from 19 different databases (including GO and KEGG). Some of these sets are highly curated collections for one specific...biological area (such as metabolism) while others are larger (~6K gene sets). The distribution of gene sets per database is: > stem(tbl) The decimal point is 3 digit(s) to the right of the | 0 | 01122333446688…

updated 15.3 years ago • Max Kuhn

belonging to approximately 6 different cancer subtypes. Essentially, I am hoping to first identify "gene modules" of gene expression corresponding to a specific cancer subtype, or groups of subtypes. (e.g. present only in A and...B cancer, but not in C, D, E or F). Subsequently, I wish to label these modules by gene ontology. (e.g. "T-cell response" module) I tried a non-R program (GenXpress) wh…

Genetics Clustering Cancer goCluster Genetics Clustering Cancer goCluster

updated 21.1 years ago • Min-Han Tan

in case I could generated them in an other way to get all the FDRs and fold changes for each gene. > class(Bgene) [1] "list" > names(Bgene) [1] "ttAll" "DownSameUp" > names(Bgene$ttAll) [1] "T11" "T3" "T19" "T19_T11" > names(Bgene$ttAll[1...FDRup" "FDRlow" For example, I want to get all the FDr for time point T11 with the respective gene name F…

limma ASSIGN limma ASSIGN

updated 19.4 years ago • daphne mouzaki RI

div class="preformatted">Dear BioC I would like to use biomaRt to get entrez gene (or other) identifiers for small tag sequences. I use the getFeature function for this. It seems that it will retrieve...band strand start_position end_position #1 66501 1700029H14Rik RIKEN cDNA 1700029H14 gene #[Source:MarkerSymbol;Acc:MGI:1913751] 8 A2 -1 #13550710 13562382 # e…

biomaRt biomaRt

updated 18.4 years ago • Hoen, P.A.C. 't HKG

T 7366 T>A 1140 T>C 8198 T>G 1830 My concern is, along with the position i want the gene names so is it possible to get the gene names from SigProfilerMatrixGenerator output ? and if not that whats the other...way to get the gene names from VCF files

BioCor StarBioTrek MatrixGenerics

updated 2.3 years ago • karmasstark

<div class="preformatted">Hello everyone, Well I am aware of some packages in Bioconductor that are useful for measuring the GO or KEGG gene enrichment in a given file for a given genome, GOstats, GSEA etc .. My question is : I am working with 4 differents genomes, I have...Well I am aware of some packages in Bioconductor that are useful for measuring the GO or KEGG gene enrichment in a g…

GO genomes GO genomes

updated 14.7 years ago • Radhouane Aniba

div class="preformatted">Hi, I have genome wide gene expression time series data for 4 time points,i have also multi variables for each of time point related to cell cluture...conditions so have tables as follows time1 time2 time3 time4 Var1 Var2 Var3 Var4 and gene expression table cell line1 gene1 ...geneN cellline2 gene1 geneN I would like to relate gene expression wi…

updated 11.7 years ago • chris Jhon

Is there any database that correlates annotation of a set of genes or gene ontology with the upstream regulatory genes (e.g. transcription factor)? Thanks

gene regulatory network

updated 8.0 years ago • johnnytam100

When I was doing GO and KEGG enrichment, some weird things happened. I used all the differential genes to do the enrichment, only 6.99% of input gene IDS are fail to map. But when I separated the upregulated genes and downregulated...genes from all, and did the enrichment separately, 8.03% of input gene IDS are fail to map for downregulated genes, 8.09% of input...gene IDS are fail to map for upr…

RNASeq

updated 4.1 years ago • waltsonwang88

I do have a bunch of genes ( nearly ~50000)  from the whole genome, which read in genomic ranges I just wondering is there an efficient way to find...__overlapped, upstream and downstream genes for each gene in the granges__ For example, assuming all\_genes\_gr is a ~50000 genes genomic range, the result I want like...idx] other_genes <- all_genes_gr[-idx] n <- coun…

genomicranges geneoverlap findoverlaps

updated 9.8 years ago • yao.h.1988

save(Sc.gsc, file = "Sc.gsc.Rda")</pre> Now, if I'm not wrong I must select the universe of genes present at my experiment. I have a list of characters with the genes that are present in my experiment and have a value...this means the value is not NA).  The problem is that I'm not being able to properly filter the genes on my experiment (variable filtered\_universe). <pre> …

gostats

updated 10.9 years ago • nonCodingGene

<div class="preformatted">hi all, i'm trying to get a function working that queries pubmed with any string and returns pubMedAbst objects corrresponding to the pubmed article hits from the query string... this is my code so far, based partly from annotate's 'query.pdf' and also from the perl script from NCBI at http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html : library…

updated 20.2 years ago • Ken Termiso

0500 > From: Jenny Drnevich <drnevich at="" illinois.edu=""> > Subject: [BioC] how to test for genes of interest? > To: bioconductor at stat.math.ethz.ch > > Hi everyone, > > I've always heard that one of the ways "around...testing > problem of microarrays is for you to a priori identify a particular > list of genes you're inter…

Normalization Preprocessing limma Normalization Preprocessing limma

updated 17.5 years ago • Gordon Smyth

a sce object and after normalization and doing all the preprocess I realized that I have duplicated gene ID's ![][1] The X column is the gene ID, and the rest are cells (this means that I have a Gen-Cell matrix) since the dimention of this...matrix is large (4999 genes and 5447 cells) it is not easy for me to visualize all the cells. Also I made the sum of each row and I get different values

SingleCell SingleCellData

updated 3.3 years ago • Romina

Hi, I am doing RNAseq Analysis and I created list of differentially expressed genes and list of Gene Ontology. However, Gene Ontology looks like this:  <pre> Term Ont N Up Down P.Up P.Down GO:0000278 mitotic...cell cycle BP 721 119 1 1.22e-16 1.00e+00</pre> I can see how many numbers of genes a…

rnaseq gene ontology

updated 7.6 years ago • karagozeylul

span style="background-color:rgb(254, 254, 254)">In GRN, every gene interacts with every other gene or sometimes with itself too and every gene connects with other genes with different

microarray gene interaction GRN

updated 10.2 years ago • shaheryar

cell type having >=5 replicates. For my biological question, I need to identify the unregulated genes of each cell type and the genes do not have to be differentially expressed compared to all the others or cell type specific...1) I ranked all the genes within each array and would like to identify the genes that are consistently ranked in the top 50% of all the genes. What...statistical me…

updated 14.2 years ago • Wendy Qiao

I am using DEseq2 to quantify the gene expression of a very limited set of non coding genes. <span style="line-height:1.6">It might be obvious, but can I still trust...the significance of the differential expression that I obtain, or would having a limited set of genes cause some genes that are not strongly differentially expressed to appear as significantly differentially expressed...span…

DEseq2 differential gene expression

updated 9.4 years ago • dmr210

<div class="preformatted">Hello, I am trying to identify all putative GATA binding sites in the mouse genome. Ideally, I want to get genomic coordinates for each "binding site" to enter into a GenomicRanges object (I know there will be a lot of hits) and to overlay this information with the results of a ChIP- Seq experiment. Seems that there are multiple packages to try and do this with, …

RMAPPER GenomicRanges RMAPPER GenomicRanges

updated 14.8 years ago • Ravi Karra

the vignette (I'm using data from a self spotted microarray with oligonucleotides which I mapped to Entrez geneIDs): >library(AnnotationDbi) >makeHUMANCHIP_DB(affy=FALSE, prefix="HighDensityArray", fileName="high_density_array_oid2eg.txt...categoryName="GO") >hgOver.BP<-hyperGTest(paramsBPover) and I got the result: >hgOver.BP Gene to GO BP test for over-repr…

Annotation GO AnnotationDbi Annotation GO AnnotationDbi

updated 16.8 years ago • Wiebke Iffert

data. I don't want to perform pathway analysis, only get an overview how the expressed genes are related and take advantage of the nice visualization of up and down regulation by the different treatments...species, so not present in the Kegg database. That might be part of the problem but very few genes map on the pathways... If I use kegg mapper for example, I get many…

pathways high-throughput transcriptomics nonmodel species

updated 7.7 years ago • monteiro

div class="preformatted">hi all, is there a simple way to calculate how many entrez id's are mapped to a given GO node for for a given species? thanks ariel./ </div

GO GO

updated 18.5 years ago • Ariel Chernomoretz

c())` function: you can plot the output either as `y = count` or `y = ratio`. What is the gene ratio here exactly? I can't seem to find a clear answer for this. Is it the number of genes in your data that are found in a particular...gene set, then divided by the total number of genes in that gene set (the gene set coming from the library/database you selected

plotEnrich enrichr

updated 2.9 years ago • marinaw

a code indicating what kind of evidence supports the association of the GO identifier to the Entrez Gene id. The evidence codes in use include: IMP: inferred from mutant phenotype IGI: inferred from genetic interaction

GO GO

updated 12.7 years ago • Peter Langfelder

div class="preformatted">Hello everyone, I'm trying to use biomaRt to simply get the Entrez Gene IDs from a list of probe ids from the Affymetrix Mouse 430 2.0 chip. When I use the getBM function, I end up getting

probe biomaRt probe biomaRt

updated 15.3 years ago • Mcmahon, Kevin

I've used BiomaRt to map Ensemble to Entrez Id's and Uniprot Accession Id's . Recently, biomart made some changes and it seems that Unimart is no longer available...nbsp;   EDIT: One thing I forgot to mention is that I could also get the protein and gene names and symbols from Unimart, which is something I'm also looking for. Thanks,  j

biomart uniprot unimart

updated 10.2 years ago • john

Hello everyone, I am a beginner in bioinformatics and doing my master thesis. I am performing DGE (Differential Gene Expression analysis) on an RNA-seq dataset. I have got around 500 genes after filtering. I also did a GSEA on these 500 genes and got around 78 enriched gene sets. But, I am not able to find the 500 genes in these 78 genesets, only 10-15 genes are found in the 78 genesets along wi…

dge gsea

updated 3.1 years ago • Lawrence

Hello, I have a question regarding pre-filtering of genes in RNA-Seq data for MaSigPro. I have filtered out genes that the counts in all samples was low. In some data sets I did not...get significant genes. I thought to further filter the data, to keep only genes had a difference above of 1.5 between any 2 samples: keep only genes...max (counts in all samples)/min(counts in all sam…

MaSigPro

updated 9.9 years ago • GFM

<div class="preformatted"> Hello all, I have a question while I am using the limma package to identify differentially expressed genes: should I perform gene filtering after normalization to exclude genes that are likely unexpressed in the samples before fitting the linear model. With my limited stats knowledge, I believe the inclusion of 'unexpressed' genes may affe…

Normalization affy limma Normalization affy limma

updated 16.3 years ago • Peng, Fred

I want to calculate the total length of genes (including introns) from the start codon to the stop codon.  I have loaded a GFF file into R using the GenomicFeatures...package.  Using genes(txdb) I get the output below that shows the positions of the first nucleotide of the start codon and the last nucleotide...of the stop codon.  Is there a function in GenomicFeatures t…

genomicfeatures gene size gene length

updated 8.3 years ago • ehimelbl

Hi Group, Is there any function which would help in converting data from probe level to gene level by averaging the expression of all the probes corresponding to a gene. For eg: array1 array2 probe 1 Gene 1 2 4 probe...2 Gene 1 4 3 probe 3 Gene 2 5 4 result: array1 array2 Gene1 3 3.5 G…

updated 15.0 years ago • viritha kaza

<div class="preformatted">hi, I have generated a list of significant genes for 3 time points separately using the function "decideTests"in Limma package.Using this function I generated foldchanges and FDR for every gene using method Benjamini and Hochberg ("BH") and p.value=0.05. I was wondering if it is possible to generate all the FDR and foldchanges...div class="preformatted">hi, I …

limma limma

updated 19.4 years ago • daphne mouzaki RI

div class="preformatted">Hello, I have a gene list with each genes location and I would like to plot an ideogram with shows where each of these genes are located. What

Cancer Cancer

updated 16.2 years ago • Daniel Brewer

What is not clear to me is on what basis to chose `m1` which is the "expected number of prognostic genes". Is it the number of significant genes I identified in my own dataset? For the example below, the power increases when I...two groups) for `est_power_distribution()` as for `estimate_samples()`? ```r # Estimate the gene read count and dispersion distribution dataMatrixDistribution = es…

RnaSeqSampleSize

updated 4.6 years ago • Matthias Munz

Hello, I would like to use EDASeq for gene length normalization for RNA-Seq analysis. However, I have a basic question: According to the manual, the "getGeneLengthAndGCContent...help us retrieve the gene length and GC content of our gene of interest but, how can I use it to download all the genes information instead of some...genes for human? Thanks

edaseq r rna-seq

updated 5.7 years ago • karla.ruizce30

when answering the question. for my experiment i first have to run an in silico analysis on several gene expression datas from GEO and ArrayExpress. i wanna check the biologically meaningful differential expression between...samples ( which are gene expressions from 3 different cell types) and then to visualize the data more explicitly i wanna do gene enrichment and

microarray microrna

updated 9.1 years ago • n3da.karami

Hi everyone, I have to perform Gene Ontology in those data which are **Locus ids** coming from *Streptococcus Pneumoniae*: **Advantageous**= SP_0660, SP_0789, SP_0829...Hi everyone, I have to perform Gene Ontology in those data which are **Locus ids** coming from *Streptococcus Pneumoniae*: **Advantageous**= SP_0660, SP_0789, SP_0829, SP_0834, SP_0873, SP_0894, SP_0902, SP_0914, SP_0947, …

GO GeneOntology LocusIDtogeneIDconversion

updated 3.3 years ago • BioinFo.X

This works well and shows what I want it to. My issue is, I need to extract the gene ID's that are shared across three time points: 40-min, 120-min, and Recovery. I do not want to observe the genes that overlap...control. Is there a method of doing this? I understand the *intersect* function can intersect the genes, but I seem to only be able to do this for all 4 time points at once. A…

ggvenn

updated 3.7 years ago • axe880

generated transcripts file in gtf format. I wondering if I can use any R package to convert it to gene level gtf file. By this means all the transcripts are collapsed into genes and each gene contains all the exons seen in...all the transcripts for that gene. Sample Data attached. In the attached GTF file I have 3 made up transcripts from 2 genes. What I?would want to get as a output...is a gtf…

convert convert

updated 14.0 years ago • Abhishek Pratap

div class="preformatted">Hello there, I have 100 lists of differentially expressed genes, and I am trying to find genes overrepresented in these 100 lists (I call them a 'cluster of genes'). What's worse, I expect not...only one cluster of genes, but three or four or five of them. That is why, a simple intersection() will not help. I wish to had a function that can select...all genes which ap…

updated 17.3 years ago • Heike Pospisil

Help me to compare genomes and find out the species-specific genes among genomes. I want to compare two genomes and find out genes that are available in one genome but not available in another

NextGenerationSequencing genomes GenomicSequence

updated 2.1 years ago • abhisek001

div class="preformatted">Dear all, there is the possibility with bioconductor if i have a list of gene (affiID,....) to know if this gene are involved in a disease: for example cardiovascular disease? Best regards. -- ----------------------------------------------------- Dr. Alberto Goldoni

updated 15.9 years ago • Alberto Goldoni

t tested, so minor modifications may be required. tp <- topTags(lrt, n=15) # Extract the top 15 genes de_counts<-dge$counts[row.names(tp), order(dge$samples$group)] # Get raw counts for top genes rs<-rowSums(de_counts) # Assuming...all samples top.names <- names( rs[ order( rs, decreasing=TRUE ) ] ) de_counts[top.names, ] # DE genes Ranked ,highest first Thanks, Shre…

updated 13.1 years ago • Shreyartha Mukherjee

reference genome using STAR and I used featureCounts to quantify the reads mapped to the reference genes and found the gene counts. Before I start the deferentially expression analysis, I would like to find the expressed genes...I use the command below and found 15463 genes, is it right to say, out of 24321 genes 15463 genes are expressed. dds<-dds\[rowSums(counts(dds)) > 0,\] dds…

deseq2 rnaseq differential gene expression featurecounts rnaseqGene

updated 7.0 years ago • melkile26

Gene ontology testing with `goana` gives me an error for a specific coefficient of interest, but not the others in my data. For...https://github.com/nztao/goana_issue_example fit.example <- readRDS("goana_issue_example.rds") # Gene ontology testing with goana # Example: Coefficient of interest [1] gives error, but [2:6] do not go <- c() go <- goana(fi…

limma

updated 3.4 years ago • neilzhao

<div class="preformatted">Hi, I have a simple problem that's driving me nuts... Any hints are appreciated! I am retrieving the human homologues of rat genes. I use the functions 'getHOMOLOG' and 'listToCharacterVector' from the library annotationTools. Everything is going fine, except for one thing: Some rows (genes) contain multiple entries (homologues); for such row I would like to get r…

convert convert

updated 12.9 years ago • Guido Hooiveld

hgu133aACCNUM, ifnotfound=NA))); You want to use EntrezGene identifiers to define the selected gene list and the gene universe. So you want: geneSample <- unlist(mget(affySample, hgu133aENTREZID)) ## but should still filter...You don't need the hgu133acdf package for this. If you want to use as your universe all genes probed on the chip, then you can do: c…

GO Cancer cdf GOstats GO Cancer cdf GOstats

updated 18.6 years ago • Seth Falcon

Hi I am using the WGCNA package and the authors recommend that we filter genes according to their mean expression or variance since low-expressed or non-varying genes would represent noise. What

WGCNA

updated 3.7 years ago • María José

I am trying to extract genes coding "lncRNA"s from a huge dataset. There are about 40,000 genes with the ensemble ID. I can't search all of them on the website

ncRNAtools RNASeqData

updated 3.8 years ago • sushimoto

div class="preformatted">Hi list How do i find common genes between different datasets? peevi [[alternative HTML version deleted]] </div

updated 15.0 years ago • Peevi Ijkl

<div class="preformatted">Hi, I sincerely thank Dr.Brown for his response to my earlier post on design matrix. I have two questions....1. about the discrepancies in my DE results 2. B-values These are my target files FileName Cy3 Cy5 Original Names HIDEN_1.gpr Ref HI_Inf Heat_Inactivated_1 HIDEN_2.gpr Ref HI_Inf Heat_Inactivated_2 H…

updated 14.9 years ago • Prasad Siddavatam

HTSeq-count with the option `-s reverse` and `mode unique`. When I checked the counts of some genes I found that the number of counts are different between htseq-count and summarizeOverlaps. For example for two overlapping...genes but that are on different strand I obtained the following values: Gene_name Strand SummarizeOverlaps HTseq-count...3231 Subsequently, I visua…

genomicAlignments summarizeOverlaps

updated 5.5 years ago • dequattro.concetta

How could one produce a set of faceted-by-gene plots of UMAPs, each one showing a gene's abundance as the colour scale? `colour_by` accepts a single gene synbol but not a...gene set

scater

updated 23 months ago • Dario Strbenac

Hi! I have a list of genes, but i a havent got any values for the genes. I want to put the genes in GO(gene onthology) groups. How can i do that without any

gene ontology genefilter

updated 10.3 years ago • kanacska

not find the good answer for that. Sorry for the re-post :( suppose i have some probes for the same gene, I am wondering which is the proper way to get a statistic for the expression for this gene? using mean, median or max or min...but I wondering if there is some ref on it. btw, is there some ref on the data pre-processing (gene selection, multiple comparison, better with case study) for micr…

Microarray Microarray

updated 19.2 years ago • Weiwei Shi

Hello, I am a little confused with the classification of genes in TissueEnrich: > Tissue Enriched: Genes with an expression level greater than or equal to 1 (TPM or FPKM) that also have...levels in a particular tissue compared to all other tissues. Another: > Tissue Enhanced: Genes with an expression level greater than or equal to 1 (TPM or FPKM) that also have at leas…

TissueEnrich

updated 5.4 years ago • xiaoxiaoxiaobu

Hi all,     I have a DE gene dataset and I would like to know which TFs have binding sites at the promoters of these genes. I found a list of 615 human...TFs on the GSEA website with the genes they bind to, but my DE gene list is too large to manually test. I then thought to create custom GO terms using each the TF...target genes, but that also would take too long (615 TFs). Do…

GSEA transcription factor binding site enrichment analysis

updated 7.2 years ago • tkapell

I tried to find non-DGE genes from both microarray and RNA-seq. The definition I used is to find gene which has logFC small and close to 0. I found that...if the gene has small logFC, the p-value tend to be big (>0.05). I found that after I filter the logFC and tried to visualize the distribution...of p-value. My question is, if I keep this genes and said this is the genes that is not DE b…

limma rnaseq microarray

updated 10.1 years ago • bharata1803

Hello, I am using a gtf file in the homepage of iGenomes for bulk RNA-seq of the whole brain of drosophila (Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf). I did the annotation using Rsubread and got a file with gene symbol. However, there are some genes of one spelling but the first letter is either uppercase or lowercase. They are with different gene ID (e.g. Crc and crc). …

Drosophila Rsubread dm6

updated 3.7 years ago • Chise