Questions tagged [gene-expression]
The gene-expression tag has no usage guidance, but it has a tag wiki.
80
questions
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30 views
mapping snp variants to gene expression data
I have a list of SNPs associated with a trait and I'd like to create a list of up- and down-regulated genes associated with these SNPs (using eQTL data I guess). What's the fastest way I could go ...
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21 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:
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1answer
39 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:
...
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24 views
Different results in Differential Expression analysis of Microarray Data
I'm new to R, so be patient with me.
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 ...
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18 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 ...
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2answers
96 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 ...
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1answer
41 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 ...
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0answers
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 ...
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0answers
10 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 ...
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1answer
158 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 ...
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5answers
141 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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1answer
44 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 ...
3
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1answer
241 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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1answer
44 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 ...
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1answer
45 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 ...
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2answers
62 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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1answer
25 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 ...
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1answer
37 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 ...
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23 views
How to merge several microarray-based gene expression datasets while not excluding genes that are not present in all datasets?
In integrative gene expression analysis when two expression matrices from different datasets are merged together, they are usually merged by common genes in both expression matrices while all other ...
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1answer
50 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 ...
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0answers
62 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 ...
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0answers
27 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 ...
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0answers
18 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 ...
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1answer
42 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 ...
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3answers
66 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? ...
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1answer
42 views
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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1answer
40 views
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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2answers
930 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? ...
2
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1answer
91 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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0answers
20 views
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, ...
0
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1answer
34 views
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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1answer
109 views
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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1answer
375 views
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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1answer
171 views
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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0answers
35 views
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 ...
3
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1answer
90 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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95 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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1answer
41 views
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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2answers
55 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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29 views
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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2answers
141 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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0answers
247 views
How to convert Illumina IDs to Gene Names?
I am new to the area of bioinformatics, so apologies if this is too obvious of a query.
I need to analyze the RNA Seq data from GSE98455.
The dataset is of the following format:
...
2
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1answer
615 views
How to downsample some of the samples in RNA-seq data?
I have 40 samples and these are into two groups. I would like to perform a differential analysis between two groups. The library size of the samples is very low. But there are two samples (GroupA_12 ...
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1answer
90 views
Available phenotype data from GTEx
I am using gene expression data from the The Genotype-Tissue Expression (GTEx) project, available here: http://gtexportal.org. I would also like to use phenotype data for each sample (especially age, ...
2
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0answers
98 views
How can I collapse probes to single value per gene using GEOquery?
I have extracted microarray gene expression data from GEO using the GEOquery package in R. There are multiple probes per gene. Is there a way to select the best ...
2
votes
1answer
487 views
How to download RNAseq gene expression data from GTEx
I would like to download RNAseq gene expression data from GTEx from the liver only. What is the best way to do this?
I have tried a few things. I downloaded several files from the GTEx website (https:...
2
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1answer
321 views
How to calculate fold change in gene expression from RSEM (RNAseq)
I have gene expression data from RNAseq, specifically: log2(x+1) transformed RSEM normalized counts.
How can I convert these data from multiple samples to determine fold change in gene expression?
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1answer
67 views
HTSeq-count is returning 0 for every gene, instead of expression value
(Ported from stack overflow)
I'm trying to summarize gene count using htseq-count; and it's returning 0 counts at every gene. I'm not sure what I'm doing wrong; I think it has to do with the gene ...
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2answers
46 views
How to exclude the repetition of gene-gene correlation calculation in python?
I am trying to make a paired matrix of gene-gene correlation. Considering that I have a huge matrix (13000 genes and 900 samples) and for some reasons I don't want to decrease the number of my genes, ...
0
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1answer
296 views
Interpreting a kernel density function plot of gene expression
I need help interpreting a kernal density plot and a histogram of this data. I have provided some context below let me know if you need more information
A co-worker that I am collaborating with has a ...