Hot answers tagged

11 votes

Converting Gene Symbol to Ensembl ID in R

You can use the standard annotation package for humans (you can also use biomaRt, but it can be more confusing, see below): ...
user avatar
  • 4,622
10 votes

How to detect a mutation and predict its consequence?

I'll follow up to the great answer from Kamil S Jaron: Regarding predicting what the variant ("mutation" is a very loaded term) will do, there are a variety of tools. Chief among these are annovar ...
user avatar
  • 19.3k
10 votes
Accepted

Can exons be located outside of the coding sequence?

Yes, of course. Exons are not limited to the protein coding regions. Many UTRs are in exons. In fact, you even have various cases of UTRs being multiple exons, and being spliced. What is strange in ...
user avatar
  • 7,957
10 votes

Are gene names same across species?

Gene names are not consistent across species. Most of the time genes are automatically annotated and the algorithms try to give names that are similar to their matches in other organisms, but not ...
user avatar
  • 11.5k
9 votes

How to detect a mutation and predict its consequence?

Part 1 : how to detect mutations The keywords you are searching for are "variant calling". Basically you have to map sequencing reads to a reference genome (or gene) and then estimate for each ...
user avatar
  • 5,287
9 votes
Accepted

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

There are multiple ways to do this, and multiple protein interaction databases besides the ones you mentioned, such as BioGRID or IntAct. Interaction databases are different in how interactions are ...
user avatar
9 votes
Accepted

How to read and interpret a gene expression quantification file?

The first column contains Ensembl gene identifiers, and the suffix is a version number that can be used to track changes to the gene annotations over time. From the Ensembl Stable IDs documentation: ...
user avatar
9 votes
Accepted

Converting gene names from one public database format to another

I tend to use Ensembl Biomart for such queries since there are APIs for various programming languages, e.g. biomaRt, and, maybe more interestingly, via a REST API (although it’s a pretty terrible one)....
user avatar
8 votes
Accepted

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

International Mouse Phenotyping Consortium is building a database of phenotypes and knock-outs of mouse. I believe that this database will be fairly complete (20000 knock-outs), but these are knock-...
user avatar
  • 5,287
8 votes

Converting gene names from one public database format to another

If you're comfortable doing a little programming, check out mygene.info (web services for gene annotations of all sorts). ID translation is specifically one of the use cases addressed in the ...
user avatar
  • 81
8 votes
Accepted

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

I wonder if there is a simpler solution recently? (and hopefully, I can solve it within the scope of python. ) A simpler solution, I don't know... but this is at least one Python solution using ...
user avatar
  • 366
8 votes

Retrieve detailed gene descriptions

Description of how to use biomaRt here. Filter by your list of gene IDs. Get the descriptions etc as attributes. Eg: ...
user avatar
7 votes
Accepted

Why are some of the gene peptides returned by biomaRt missing an asterisk in the end?

If it's 3' incomplete that means the evidence used to create it was a fragment. Here's the evidence used to construct BRCA1-214 ENST00000477152.5, a 3' incomplete. You can see that there's a full ...
user avatar
7 votes
Accepted

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

As others have mentioned in their answer, bioMart is usually the best place to go for this infomation because it draws its data directly from the Ensembl database. However, you will find you do not ...
user avatar
  • 3,201
7 votes

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

Conversion using R: ...
user avatar
  • 2,564
7 votes

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

I can show you a simple way in R, using biomaRt. Let's say you have two snp ids you want to exmine. ...
user avatar
  • 3,521
7 votes

How can I calculate gene_length for RPKM calculation from counts data?

Here you can find some example R code to compute the gene length given a GTF file (it computes GC content too, which you don't need). This uses one of a number of ways of computing gene length, in ...
user avatar
  • 19.3k
7 votes
Accepted

Retrieve detailed gene descriptions

MyGene.info Using the R package for the MyGene.info database: ...
user avatar
  • 2,564
7 votes

Can exons be located outside of the coding sequence?

Those are the untranslated regions (UTRs). All mRNAs have a 5' UTR and a 3' UTR. These give the ribosome something to grab onto and often contain important regulatory sites such as miRNA target sites.
user avatar
7 votes
Accepted

How to identify gene expression signatures from gene expression data?

There is no golden/standard way to define a gene signature but they are completely different from a gene set enrichment analysis (GSEA). I will start with how to obtain a gene signature: Usually this ...
user avatar
  • 4,622
6 votes

Basic questions about GSEA

You seem to refer to the GSEA provided by the Broad institute, (there are other GSEA algorithms). 1) You can provide whatever you wish, but if you want to know if those gene sets in which side of ...
user avatar
  • 4,622
6 votes

Basic questions about GSEA

Use the following R package for Gene Set Enrichment analysis of RNA-seq data: seqGSEA There is another R package (fgsea) recently published called "Fast Gene Set Enrichment Analysis" by Alexey ...
user avatar
  • 584
6 votes
Accepted

Do any publicly available databases detail protein structure and functional domains?

Some of this information (at least some domains, active sites, etc) is available from UniProt. If you want to download their whole database, you can search without specifying any terms and then click ...
user avatar
  • 315
6 votes

Melt p-values for CpG sites mapping to the same gene

Methylation levels have high local correlation, so Fisher's method would be problematic. Having said that, you have no reason to use Fisher's method after a paired t-test. A paired t-test will give ...
user avatar
  • 19.3k
6 votes
Accepted

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

The ID you need is the NCBI gene ID, which is the same as the EntrezGene ID.
user avatar
  • 3,201
6 votes
Accepted

Writing a perl script to holding information for two genes

Perhaps this small test script will help demonstrate some of the principles: ...
user avatar
6 votes

Converting Gene Symbol to Ensembl ID in R

I tried several R packages (mygene, org.Hs.eg.db, biomaRt, ...
user avatar
  • 161
5 votes

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

Many interaction databases now work with PSI format files. Most of the main databases can do this and the EBI has set up PSICQUIC View, a very useful page where you can query multiple databases at ...
user avatar
  • 7,957
5 votes
Accepted

SNP-phenotype association analysis only using the SNPs on a specific gene

I know that the GWAS association p-value threshold is 1e-8 This may be a common threshold of statistical significance that is used, but it's definitely not an absolute value. It's a hack to try to ...
user avatar
  • 11.5k
5 votes

Identifying relevant SNPs from a list

What you are looking for is SNP annotation. If you have the chromosome:position reference and alternate alleles for your SNPs of interest, it can be as simple as uploading them to the variant effect ...
user avatar
  • 393

Only top scored, non community-wiki answers of a minimum length are eligible