macarthur-lab / gene_lists Goto Github PK

Would it be possible to add a license file? It would help clarify reuse.

In the README file the table describing the lists has a couple of rows for which the description and references include something like "union of previous lists" or "see previous lists". This makes it hard to reliably extract list metadata: the order of the lists in the table is presumably not guaranteed, and this indirection is not really necessary anyway.

I'd suggest making sure that each row is self-sufficient, with explicit descriptions (e.g., "union of gpcr_guide and gpcr_uniprot") and complete references, even if this risks duplicating information. That way when a list's metadata is extracted from its table row, there will be no need to refer to other rows in order to get the complete information.

Add the NIH LINCS Program landmark genes to gene_lists

The list of 978 landmark genes is here:

https://clue.io/command?q=/gene-space%20lm

The NIH Library of Integrated Network-Based Cellular Signatures (LINCS) Program website: http://www.lincsproject.org/

The NIH LINCS program has developed a strategy of profiling ∼1000 carefully selected landmark genes and using computational methods to infer the expression of additional target genes.

LINCS aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents.

Ref: Chen 2016, https://academic.oup.com/bioinformatics/article/32/12/1832/1743989

Just to share there is an app for all gene panels:

https://panelapp.genomicsengland.co.uk/

Genomics England PanelApp
A crowdsourcing tool to allow gene panels to be shared, downloaded, viewed and evaluated by the Scientific Community