Questions tagged [gene-expression]

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GSEA vs GSVA: Pros and cons of each method

Trying to understand when GSEA is more appropriate than GSVA and vice versa. I have seen cases when running GSEA and GSVA on the same task - compare enrichment of a geneset between two groups - gives ...
Tomas Bencomo's user avatar
1 vote
1 answer
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Multi Factor in Deseq2 Gene enrichment analysis

I want to see how the gene expression differs in breast cancer between three species, and I am using DESeqDataSetFromMatrix on my count table. ...
ToTheMoon's user avatar
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After running nf-core, is there a way to map a gene_id to a specific gene's DNA sequence?

I have been running nf-core in Python and it works great! But I have a seemingly simple question that I'm struggling to find an answer for online. After running the nf-core pipeline on my RNA ...
user18959's user avatar
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101 views

Featurecount output .txt file from bam file

After running this command: featureCounts -p -s 2 -a $genome -o $dir"/"$specie"/count_table/"$value".txt" $output_loc -T 8 on the BAM output of ...
ToTheMoon's user avatar
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1 answer
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Interpretation of clusterProfiler results

I am using clusterProfiler for differential gene expression using this code: https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html I have a question about the third line of code: <...
Sylvia Rodriguez's user avatar
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1 answer
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How evaluate biclustering algorithm over real datasets containing labels?

I have a set of real data containing labels. However, in some biclustering algorithms (e.g., Cheng and Church Algorithm), originally authors applied gene expression data like Yeast without having ...
ShokofehVS's user avatar
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1 answer
82 views

Read methylation data from tar files on GEO (GSE73303)

I'm trying to analyise methylation data using GEO, in order to conduct a multi-omics analysis. The SubSeries I am referring to is GSE73303. Unfortunately, the code used to inspect it produces empty ...
Riesz98's user avatar
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Louvain/Leiden community clustering implementation in C/C++ for gene expression data

Does anybody know of a C/C++ based implementation of the Louvain or Leiden algorithms that will take gene expression looking csv input files, with the genes in columns and the samples in rows, and ...
719016's user avatar
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Inconsistent replicate numbers in RNA-seq

I have 3 groups for the RNA-seq analysis (Control, treatment A and treatment B). There are 2 replicates for control and treatment A and 3 replicates for treatment B (lost 2 replicates due to a mistake ...
Wang Ming's user avatar
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1 answer
413 views

Determine expression values for a defined list of genes across different clusters in scRNA data using seurat

I am analyzing publically available scRNA seq datasets on R using Seurat. I have created a seurat object, clustered and annotated different cell types. Now, I am interested in comparing the expression ...
Ahmed M.'s user avatar
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Normalization and Merging of Gene Expression Panels with Overlapping Genes from Same Cohort

I have done some gene expression work using two Nanostring panels (glial profiling and neuroinflammation) on the same 18 tissue samples. There are some overlapping genes between the panels, about 150 ...
Carolyn's user avatar
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Should be RT-qPCR values standardized before PCA analysis?

I come from this question of gene exression analysis: Should PCA be standardized for gene expression? My experiment is based in 151 x 51 (individuals/samples x genes), in which, patients are subjected ...
Javier Hernando's user avatar
2 votes
1 answer
60 views

What are the conditions to perform Gene Expression Analysis on data you've performed RNA Sequence Analysis on?

I want to perform Differential Gene Expression Analysis. I recently completed RNA Sequence Analysis using the Seraut Tutorial up to this point: Finding Differentially Expressed Features (Cluster ...
Antonio's user avatar
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Could someone help me understand if all sample within this are control group?

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117872 I'm teaching myself sequence analysis. This is the count data: and then this is, what I believe to be, the coldata: All I want to know is ...
Antonio's user avatar
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Why are genetic algorithm chromosomes represented using 8 bit binary?

I am learning about genetic algorithms. Why chromosomes are represented using 8 bit binary. This arose when I apply crossover techniques to the bits. Please help me to find the answer.Thanks in ...
Julie's user avatar
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MAGs transcriptomics pipeline question

I have currently a following problem. I have a one sample that I did my metagenomics on (Illumina shotgun + nanopore) and have recovered some high quality MAGs. I also did a metatranscriptomics on the ...
Avamys's user avatar
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Is loss/gain of function reflected in RNA-seq transcript counts?

Do LoF/GoF transcripts count toward the RNA-seq TPM count? Or would these LoF/GoF transcripts only be detected by isoform quantification?
Kermit's user avatar
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how to calculate the expression values per gene for all cells

I'm currently working with a seurat object and I'd like to calculate the expression values per gene for all cells within a particular cluster. I've gone ahead and subsetted the cluster of interest. <...
mmpp's user avatar
  • 371
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1 answer
305 views

baseMean threshold

I have an RNA-seq dataset and I am using DEseq2 to find differentially expressed genes between the two groups. I used pre-filtering to remove any genes that have ...
suzie321's user avatar
2 votes
0 answers
24 views

How to retrieve Expression Atlas baseline expression results in JSON format?

I'm looking to retrieve Expression Atlas baseline expression results in JSON format, e.g. the results on this page. Several years ago I did a similar thing but looking at differential expression ...
Cat's user avatar
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Can I use a benchmark to choose a clustering or module detection method for a gene dataset?

The paper A comprehensive evaluation of module detection methods for gene expression data says that: "We first want to provide an overview of the characteristics and performance of current module ...
Lara's user avatar
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Missing value imputation method for gene expression data

I am new to working with gene expression data sets and am wondering what is the most standard or best way to impute missing values in a gene expression data? I got mine from the GEO database and the ...
b14108's user avatar
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2 votes
1 answer
144 views

Querying The Cancer Genome Atlas (TCGA) for gene expression

The UCI gene expression cancer RNA-Seq ​dataset (https://archive.ics.uci.edu/ml/datasets/gene+expression+cancer+RNA-Seq) consists of 5 types of cancers (BRCA, KIRC, LUAD, COAD, PRAD) and gene ...
fuad021's user avatar
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2 answers
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What could explain the difference in RNA-seq and Microarray expression levels?

What are some possible reasons why some trends observed in Microarray expression levels is not observed in RNA-seq. Example the difference between 2 cell types for a gene of interest show major ...
user305902's user avatar
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1 answer
53 views

How to compare across Microarray datasets for a gene in Mice?

How does one go about comparing expression levels of one gene across multiple microarray datasets pulled from different experiments/papers in mice? In my example, I've downloaded the expression levels ...
user305902's user avatar
0 votes
2 answers
147 views

what are the nodes and edges values in gene regulatory networks?

I am trying to find out how one can using gene expression data can infer gene regulatory network applying graph theory concepts. But I could not find a proper reference that explain how one can get ...
Raz's user avatar
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2 votes
3 answers
4k views

How to split a Seurat cluster in several subclusters?

I've analyzed my scRNA-seq data and have a couple of Seurat clusters that show more than one cell type in each cluster. (for example, cluster 9 shows both NK and CD4 cells) How can I split a cluster ...
Shani's user avatar
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1 vote
0 answers
36 views

NMF - Subscript out of bounds

I've calculated the cophenetic coefficients for the NMF of gene expression data, but is giving error when performing the clustering information step as given below: ...
Kartika's user avatar
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1 answer
262 views

NMF clustering not giving results

I'm trying to run the Non-Negative Matrix Factorization(NMF) for my Gene Expression dataset which was originally in matrix form. But it throws errors as given below: ...
Kartika's user avatar
  • 11
0 votes
1 answer
91 views

Different results in differential expression analysis of microarray data

I am performing differential gene expression analysis to microarray data for type 2 diabetes donors and nondiabetic donors. When I run the code I get some different results in each time (about 50 or ...
guest's user avatar
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0 answers
208 views

Differential miRNA expression using RPM

I have microRNA (miRNA) expression data in RPM. I would like to do differential gene expression between two groups. How can I do this? I have considered edgeR and DESeq2 in R, but it looks like they ...
Sylvia Rodriguez's user avatar
0 votes
2 answers
148 views

10X scRNAseq: Sample mix-up

The student who was working on scRNA seq of KO and WT lines has made a mistake and he mixed both lines and generate the final sequencing data. Now, we are having gene expression data but don't know ...
user3377241's user avatar
1 vote
1 answer
78 views

The biological meaning of the random variables and the responses in Seurat analysis

In the Seurat analysis, if we suppose that Xg and Xr denote the random variables that associate to the expression level of the gene g and of the gene r, respectively. Let Y and Yv represent the ...
MK Huda's user avatar
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1 vote
0 answers
12 views

How to decide whether to assume 2 Gene Losses or 1 to find minimum cost trees for Gene Duplication/Expression events?

This paper introduces an approach to estimate a convergence from discord between phylogenetic species trees and gene trees, using Gene Duplication and Expression events. A Gene Duplication (GD) event ...
Aniruddha GS's user avatar
1 vote
0 answers
19 views

How can I associate centrality score of genes(vertices) in a GRN with the probabilistic model in terms of cause and effect?

I'm learning to build Bayesian Network Based Modeling of Gene Regulatory Network of Cancerous Cellular Cells. So far, I have learned to form a Bayesian Network based on nature of genes(i.e Functional ...
Mushahid Hussain's user avatar
2 votes
1 answer
1k views

What are common ways to calculate gene length for TPM calculations? [duplicate]

I am aware of this similar question. But the accepted answer there answers how to calculate TPM given a mapping from gene name to gene length. My question is, given an annotation file of genes (for ...
user3494047's user avatar
1 vote
5 answers
829 views

Normalize RNA seq data from multiple runs for expression analysis

I have RNA samples sequenced with TruSeq Stranded Total RNA kit protocol in Illumina HiSeq (2x125bp) and NovaSeq platforms (2x150bp) - almost 100 samples altogether. I have to use the samples data for ...
Praveen's user avatar
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0 votes
1 answer
632 views

Why am I getting empty expression data from GEO?

I am trying to analyze the scRNAseq data from this study. In their Method section they write: The accession number for the RNA and DNaseq data reported in this paper is GEO: GSE116237. When I go ...
chickenNinja123's user avatar
4 votes
1 answer
255 views

Why did expression based subtypng of breast cancer gain much more acceptance than others

This is may not be entirely technical question but rather a academic question. But the technique behind the application is within the scope of bioinformatics. So I would try to ask here that: In each ...
unicorn's user avatar
  • 211
0 votes
1 answer
69 views

How to find genes whose expression vary the most in time-series?

Hi I am reading this paper and trying to analyse the same datasets in my work: dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data In this paper, the ...
Hamda Binte Ajmal's user avatar
0 votes
1 answer
98 views

Common gene naming conventions and how to convert between them

I have two questions, one is a direct question about some RNA expression data. The other is more broad, but motivated by the first. I have downloaded an expression set for a class project and I am ...
Angus Campbell's user avatar
0 votes
2 answers
83 views

Print specific columns in a matrix on the basis of sample id's in the header

I have a matrix file (expression.txt) in which the first column is a gene_id and from the second column the sample id's start. This matrix has 20,000 columns with sample id's corresponding to ...
Priya's user avatar
  • 351
0 votes
1 answer
85 views

How can I get bedtools to tell me which genes are being expressed?

I'm trying to align the Acinetobacter baumanii genome to a genome. I've already done the alignment, and I want to use bedtools to see which genes are being expressed exactly. When I try running the ...
sjgandhi2312's user avatar
1 vote
1 answer
43 views

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases ...
jasperhyp's user avatar
0 votes
1 answer
58 views

How to check if a given gene is expressed in a group of microarray samples if I do not have control group to compare with?

I have a microarray gene expression dataset consisting of placenta samples. I want to check whether these placenta samples are mixed with maternal decidua tissue. I have marker genes for decidua ...
Sashko Lykhenko's user avatar
0 votes
0 answers
548 views

Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons

i try to implement LIMMA for paired samples in order to compare gene expression before/after treatment. But...i'm not confident in my results since every single gene expression seems to be ...
Gwénolé's user avatar
0 votes
0 answers
137 views

Opening gctx files

I installed cmapPy but I don't know how to use it to read gctx files. I read the documentation. If anyone knows how to do it with cmapPy or any faster method your help would be greatly appreciated. I ...
blue bells's user avatar
1 vote
0 answers
23 views

co-expression analysis for two different tissues of same sample

I have gene expression datasets A and B that contain as many rows as genes and as many columns as samples. The rows in A and B represent a common set of genes measured in different tissues of the same ...
data's user avatar
  • 123
0 votes
1 answer
257 views

Gene expression Table to Expression Matrix converstion

I have an RNAseq gene expression file (Count data) as follows, I need to conduct a Differential gene expression analysis between Patients, for that, I need to have this file as a Matrix of Rows as ...
David's user avatar
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0 votes
4 answers
171 views

Where can I find Single Cell Data with Location "Coordinates"?

Does single cell data typically have the following meta-data: the "coordinates" (e.g. on a tissue, adjacent tissues) saying where each cell in the sample was located relative to other cells? ...
gbrlrz017's user avatar