8
votes
Accepted
6
votes
Retrieving a list of human genes having GO associations
I guess the following code will help,
...
- 604
6
votes
Retrieving a list of human genes having GO associations
Here's an example for the mouse genome:
library(org.Mm.eg.db)
select(org.Mm.eg.db, c("GO:0048406"), c("GENENAME","SYMBOL"), c("GO"))
You get output like:
...
- 19.5k
4
votes
Accepted
Obtain CD (cluster of differentiation) marker expression information
I can offer this as a way to scrape the data from the Abcam resource:
...
- 646
4
votes
Accepted
How do I get GO annotations for a list of UniProt IDs?
The link to the FTP for the GOA database files is listed on the GOA Downloads page. The file containing the mapping info you seek, goa_uniprot.all, comes in two ...
- 810
4
votes
Accepted
different results coming from biomart online and biomaRt R library
Sorry, this was my mistake in the last question. To search down the ontology, rather than just for the specific association with a term, biomaRt needs a different filter: 'go_parent_term'.
Try:
<...
- 1,749
3
votes
Accepted
Retrieve all genes for a specific gene ontology
You can use BioMart to filter by your GO term and get the genes as attributes. BioMart is ontology-aware so will pull out all genes associated with your term and with any of its child terms.
There is ...
- 1,749
3
votes
NCBI xml-format Printing nodeValues from tags with the same names
use a XSLT processor (http://php.net/manual/en/class.xsltprocessor.php) with the following stylesheet.
...
- 1,491
2
votes
Accepted
Interpreting a kernel density function plot of gene expression
There are two topics here to be discussed. Gene Set Enrichment Analysis and a kernel Density plot.
GSEA
The Wikipedia page about Gene Set Enrichment Analysis covers well the principle and the tools ...
- 4,174
2
votes
Accepted
Parsing the json file from gene ontology result into dataframe
I don't know how to do that in R but I think this is what you want:
I used http://json2table.com for view the data structure of the JSON file, then I used ...
- 769
2
votes
Analyzing proteins based on sequence similarity
I suggest you give DAVID a try. Specifically, their Functional Annotation tool. Just enter your list of protein IDs, and it will return groups of proteins where particular GO functions are ...
- 9,452
2
votes
Accepted
How to programmatically classify a protein according to its genbank feature
Using the UniProt website API (https://www.uniprot.org/help/api) this could be done with a query like
https://www.uniprot.org/uniprot/?query=name%3A%22type%20IV%20secretion%20protein%20Rhs%22&...
2
votes
Accepted
How do I perform a pathway related grouping of genes?
The DAVID tool is always interesting, and easy to try: https://david.ncifcrf.gov/gene2gene.jsp
You submit a list of genes, it uses several different annotation databases to annotate the gene list, ...
- 1,012
2
votes
1
vote
Assigning multiple GO IDs to an ID: Should I split or use the first or last ID in the hierarchy?
You might want to look at Revigo to simplify multiple GO terms into their parent terms. I've used rrvgo extensively to simplify enrichment results - this is the R implementation of Revigo.
It's not ...
- 11
1
vote
Building a group representation of genes' ontologies
Have you tried DAVID for functional annotation (Gene Ontology and KEGG terms)?
I usually use DAVID to extract GO and KEGG terms and plot the results using R.
If you also want to plot a protein-protein ...
- 313
1
vote
Accepted
RDAVIDWebService (R package) manual installation, or alternative tool
That package was deprecated in Bioconductor version 3.13 after several attempts to contact the package author/maintainer.
Your options include reverting back to Bioconductor version 3.12 or using one ...
- 535
1
vote
Retrieving all genes for a gene ontology term
It is filtering by your GO terms, it is only giving you genes associated with those GO terms. However the GO terms in the output are not linked to the GO terms in your input, so it is giving you all ...
- 1,749
1
vote
Accepted
gprofiler output ENSG to gene name
This is usually done using AnnotationDbi in combination with the annotation database for human org.Hs.eg.db.
...
1
vote
Accepted
How to identify latent variables in single-cell RNA-Seq data
I think to identify latent variables, PCA is probably not going to work. NMF might be worth trying. You might want to check out a method called consensus NMF (cNMF) (https://elifesciences.org/articles/...
- 857
1
vote
Accepted
Why are my genes filtered for Gene Ontology term enrichment?
What is "click here for details" saying? That link should contain an explanation of what happened.
GSEA usually requires entrez_id to run. If your list contains <...
- 537
1
vote
Discordance of Gene Ontology data between Mouse Genome Informatics and Ensembl sources
Short answer, we get our annotations from GOA, which has the three listed. We're in touch with GOA to see why they differ from MGI.
- 1,749
1
vote
How do i map subcellular localizations to lower the number of classes to predict
One way to do this would be to plot the first 10 GO categories of the the CC sub ontology (CC from cellular component). Or you can just visit the official webpage to see the list of children terms of ...
- 4,692
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