Questions tagged [gene-expression]

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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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DAVID returning invalid KEGG pathways in gene enrichment analysis

I'm using the latest version of DAVID Knowledgebase (v2021q4, Available at https://david-d.ncifcrf.gov) for enrichment of a set of genes that I have. Using the ...
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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 ...
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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 ...
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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 ...
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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 ...
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Extracting adjusted expression after adjusting for covariates

For a given number of features (hundreds ~ thousands protein quantifications) and samples (hundreds) I am fitting a multi-linear model where I am aiming to regress out the effect of a few covariates. ...
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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: ...
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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: ...
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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 ...
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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 ...
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2 answers
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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 ...
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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 ...
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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 ...
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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 ...
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1 vote
1 answer
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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 ...
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1 vote
5 answers
241 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 ...
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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 ...
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3 votes
1 answer
246 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 ...
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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 ...
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1 answer
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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 ...
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2 answers
65 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 ...
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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 ...
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1 vote
1 answer
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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 ...
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1 answer
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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 ...
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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 ...
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0 answers
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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 ...
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1 vote
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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 ...
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1 answer
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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 ...
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4 answers
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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? ...
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1 answer
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Looking for genes that are expressed the same in all the samples

I have 5 samples (from a RNA seq experiment) from patients but I have no control, so since we can't look for the differentially expressed genes we want to look for the genes that have similar ...
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1 answer
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gene-gene correlation from two different Tissues

I am stuck on how to do correlation for two independent data sets with common row and column names. A and B are datasets that contain as many rows as genes and as many columns as samples. The rows in ...
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1 vote
2 answers
1k views

FPKM, FPKM-UQ, TPM or counts: How do I know which kind of unit should I use?

I'm trying to download data from the TCGA for gene expression analyses in R, but I'm in doubt if I should use FPKM, FPKM-UQ or counts? When the dataset is in counts, I suppose it's raw data, isn't it? ...
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2 votes
1 answer
106 views

COVID-19 GWAS: what is a cross-replicating association?

In a genomic study of patients infected with SARS-CoV-2, the authors detected cross-replicating associations with rs11385942 at locus 3p21.31 , the association signal spanned the genes SLC6A20, ...
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What is the best approach to classify a patient cohort by the expression (low, int, high) of a single gene of interest?

I am working with a dataset of nearly 100 patients. I performed Salmon quantification with genecodeV34 and imported the results with tximeta. I normalised the TPM salmon output with TPM (using edgeR, ...
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1 answer
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P-value correction when evaluating correlation between gene and miRNA expression

First of all I apologize without the question is very basic, I am taking my first steps in bioinformatics. Data information We are evaluating the correlation (using the Pearson, Kendall or Spearman ...
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1 vote
1 answer
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What are the state-of-the-art cell-type RNA-Seq deconvolution methods?

I would like to find the proportion of each cell-type in bulk RNA-Seq transcriptomics data. I am looking for some guidance on the following: What are the state-of-the-art methods? What are their ...
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1 vote
1 answer
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What unit (TPM, FPKM/RPKM, or other) to use when working across samples

I have raw gene read counts and would like to perform an analysis across multiple samples. I've found conflicting info online on how this should be done. One commonality however is that FPKM/RPKM ...
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0 votes
1 answer
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WGCNA co-expression network analysis with less than 20 samples

I have two cancer subtypes data. Subtype A is 14 samples and Subtype B is 23 samples. I'm interested in identifying the functions of some LncRNAs in the Subtype A group. For this I'm using all protein-...
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MEME's motifs have an E-vaue too high

I'm currently learning how to use MEME-Suite (web tool) to find a specific known transcriptor binding site in the promoter region of 5 putative bacterial genes of interest, but the results obtained ...
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3 votes
1 answer
110 views

Inflated p-values in quantitative trait analysis

I am performing a quantitative trait association between the expression of one gene and ~400,000 methylation values. First, both variables are rank inverse normal transformed, adjusted for confounders ...
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0 answers
118 views

Unable to gunzip fastq files from ENA

I am trying to process fastq files in order to build gene co-expression networks (by following this tutorial). When I download any fastq file from ENA, and try to process it with the command: ...
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0 votes
1 answer
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How to understand and analyse RNA-seq data (for a beginner)?

I am trying to understand expression of a certain protein across Pseudomonas species. I downloaded an SRA file from NCBI and converted it to a fastaq file. I am not able to understand how to interpret ...
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2 answers
149 views

Tools for creating gene coexpression networks

What are some good tools (in Python if possible) for creating gene co-expression networks from RNA seq data?
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0 answers
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How do I generate a list of post-synaptic gene markers that will guide me in my search for these markers in intestinal stem cells?

I would like to generate a list of gene markers that represent post-synaptic related genes. I will then use this list to search through single cell sequencing data, in order to assess whether certain ...
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2 answers
181 views

Difference between PPI networks and Gene Co-expression networks

What exactly is the difference between protein-protein interaction (PPI) networks and gene co-expression networks? Based on my rudimentary understanding, PPIs are constructed from gene co-expression ...
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