have a look at this link:
For customized species, you can create your own gene set files for enrichment.
-
Hi uqfgaiti,
have a look at this link:
For customized species, you can create your own gene set files for enrichment. -
Gene Set Enrichment Analysis
Hi all,
I have used the cummeRbund function findSimilar() to find the 10 most similar genes to the differentially expressed genes I identified using Cuffdiff. This used the Jensen-Shannon distance and produced a ranked ordered gene list which I now want to test for GO enrichment. The file looks like this:
"XLOC_007917" 0
"XLOC_008881" 0.00417099861122699
"XLOC_017692" 0.0178758082512721
"XLOC_008901" 0.0180682577435933
"XLOC_014267" 0.0333227735282459
"XLOC_013408" 0.0400392521794019
"XLOC_013497" 0.0412541820119971
"XLOC_010554" 0.0453928603025379
"XLOC_000570" 0.0461264880687295
"XLOC_010786" 0.0469577467848723
I first searched manually for GO terms for each of the most similar genes but I'd like to do a more robust analysis. I am trying to run GSEA, the Java application from Broad Institute.
I made my Ranked list file format (*.rnk) and now I have to choose a gene set database.
I am working on a sponge species so I can't use the database already provided.
How can I create my own gene sets database? What should it look like?
Any tips or advice will be appreciated!
Thanks
Federico
-
Many organizations study rare diseases, but few have a mission as impactful as Rady Children’s Institute for Genomic Medicine (RCIGM). “We are all about changing outcomes for children,” explained Dr. Stephen Kingsmore, President and CEO of the group. The institute’s initial goal was to provide rapid diagnoses for critically ill children and shorten their diagnostic odyssey, a term used to describe the long and arduous process it takes patients to obtain an accurate...12-16-2024, 07:57 AM -
Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.
Long-Read Sequencing
Long-read sequencing has seen remarkable advancements,...12-02-2024, 01:49 PM
Leave a comment: