Showing posts from May, 2018

Get the newest Reactome gene sets for pathway analysis

For first-pass pathway analysis I find Reactome to be the most useful database of gene sets for biologists to understand. For a long time I have been using Reactome gene sets as deposited to the GSEA/MSigDB website. Recently a colleague pointed me to the gene matrix file offered directly on the Reactome webpage (Thanks Dr Okabe).

There are some differences. Firstly there are more gene sets in the one from the Reactome webpage (accessed 2018-05-09)
$ wc -l *gmt     674 c2.cp.reactome.v6.1.symbols.gmt    2022 ReactomePathways.gmt    2696 total
Secondly, there are more genes included in one or more gene sets:
$ cut -f3- c2.cp.reactome.v6.1.symbols.gmt | tr '\t' '\n' | sort -u | wc -l 6025 $ cut -f3- ReactomePathways.gmt | tr '\t' '\n' | sort -u | wc -l 10852
And overall there are about threefold more gene-pathway entries 
$ cut -f3- ReactomePathways.gmt | wc -w 106405 $ cut -f3- c2.cp.reactome.v6.1.symbols.gmt | wc -w 37601
I also looked at whether the gen…

Publishing datasets on the dat network - benefits and pitfalls

As I mentioned in an earlier post, Dat is a new data sharing tool that uses concepts of bittorrent and git to enable peer-to-peer sharing of versioned data. This is cool for sharing datasets that change over time, because when you sync the dataset, only the changes are retrieved, sort of like git. As it uses peer-to-peer technology, it is fairly resilient to node failures as the datasets are mirrored between peers. The "dat publish" command registers the repository on, meaning that the files can be retrieved by anyone via a normal browser.

To demonstrate, I have released the bulk data dumps from my RNA-seq data processing project, DEE2, which consists of 158 GB of gene expression data. These data are freely available via a browser at or by using the dat command-line tool.

If you're after a single file, then you can use the following syntax to retrieve over https:

wget<long dat address>/<file…