Questions tagged [gene]

Use this tag to refer to the gene sequence/coding part of the sequence.

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7
votes
3answers
3k views

Retrieve detailed gene descriptions

Given a list of gene IDs, how do you retrieve the gene description, summary and other detailed information in R?
4
votes
1answer
878 views

Inspection of gene expression in scRNA-seq data

I am running the data preprocessing pipeline for scRNA-seq data presented here. 3.8.6.1 Gene expression In addition to removing cells with poor quality, it is usually a good idea to exclude genes ...
-1
votes
1answer
99 views

Converting gene symbols between species

I have a list of genes in a mouse model How I can find the equivalent gene symbol/name for human from them? This is my list ...
12
votes
6answers
1k views

Converting gene names from one public database format to another

This is a question from /u/apivan19 on reddit. The original post can be found here. I have some proteomics data that was given to me with the UniProt gene identifiers in column 1. I've been trying to ...
10
votes
4answers
739 views

How can I build a protein network pathway from a gene expression quantification file?

Assume I have found the top 0.01% most frequent genes from a gene expression file. Let's say, these are 10 genes and I want to study the protein protein interactions, the protein network and pathway....
5
votes
3answers
187 views

Where can I find a database that has phenotype information together with associated SNPs?

I have been searching for a long time and the furthest I got is some database with the functional description for genes. Then, I have to parse these descriptions manually to figure out the association....
11
votes
1answer
882 views

How to read and interpret a gene expression quantification file?

I have a gene expression quantification file from TCGA that contains the following lines: ...
5
votes
6answers
4k views

How to get a list of genes corresponding to the list of SNPs (rs ids)?

Is there a way for me to get a list of genes given a list of SNP rs ids? I found several questions asked with a similar goal years ago, and the answers are always about using multiple online tools, ...
4
votes
1answer
183 views

Duplicate gene symbol handling in GEO gene expression data

I have downloaded a gene expression data from GEO database (GSE3268) in which in some of its rows there are duplicate gene symbols. For example TP53 exists in two rows with different expression values ...
4
votes
3answers
371 views

Expression of a gene in different groups

I would like to check the expression of a gene in different groups like Disease vs Normal samples. I want to make a plot out of that to check whether it is significant or not. From this paper lncRNA ...
3
votes
1answer
856 views

Missing data mappings in mygene.info while trying to convert Genes Ensembl Ids to Entrez Ids

I need to convert a lot of Ensembl Ids to the relative counterpart in Entrez (e.g., ENSG00000157764 > 673). I found mygene.info ...
1
vote
2answers
41 views

Multiple Alignment cost application

Is there any biological application/case where someone would be interest in the estimated total cost of the alignment between a set of sequences (genes or amino acids) without the aligned sequence ...
1
vote
2answers
408 views

How can I find out if my gene of interest is duplicated?

To identify homologous genes, I performed tBLASTn analyses against my genome of interest resulting in sequences of a closely related species. Using this method, I found two (and in some cases up to ...
1
vote
1answer
53 views

How to identify genes from a genome assembly of C. Elegans?

I have two full genome assemblies for C. Elegans samples collected from two different geographical areas that I found on WormBase. These are in fasta format. I want to go gene-by-gene and compare the ...