Reactome Species Comparison – analysis table
I’m trying to find a way to extract % orthologous genes in a pathway from human to an organism of choice. Previously this seems to be possible, as this 2011 paper is suggesting (analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.201100066):
BASIC PROTOCOL 5 COMPARE INFERRED MODEL ORGANISM AND HUMAN PATHWAYS USING THE SPECIES COMPARISON TOOL
The comparative analysis of pathways and biological process offers important information on their evolution, supports metabolic engineering and the study of human disease. Reactome uses manually-curated human pathways to electronically infer equivalent events in 20 other species. The Species Comparison tool allows users to compare the predicted model organism pathways with those of human to find pathways conserved (or not) between both species.
Necessary Resources Hardware Computer capable of supporting a Web browser and an Internet connection Software Any modern Web browser such as Firefox, Safari, Chrome and Internet Explorer will work to display Reactome web pages. Point the browser to the Reactome home page at www.reactome.org. In the sidebar of the home page, click the “Compare Species” button to launch the data selection page for the Species Comparison Analysis. On the “Species Comparison” page is a selection tool that reveals a drop-down list of species. Select species “Mus musculus” from the drop-down menu and click the “Apply” button. After a few minutes, a table of results entitled “Species Comparison” will appear. The “Species Comparison” results are presented as a sortable table that can be downloaded for further analysis or record keeping. The table contains one row for each Reactome pathway. The columns represent: i) pathway name, ii) the species used for comparison with human, iii) number of proteins in the human pathway, iv) number of proteins inferred to exist in the comparison species, v) graphic representing the ratio of values in column 3 and 4, and vi) a view button that launches the Pathway Browser and displays the relevant pathway diagram. Click at the head of the column labeled “% in other species”. The table rows should reorder so that the pathways with the greatest overlap between mouse and human are at the top. Scroll down the results page and click the “View” button for the “Double-Strand Break Repair” pathway to launch the Pathway Browser in a new window, as is shown in Figure 8.7.14.
However, it seems like this is no longer possible in the current interface – or am I missing something? Many thanks!
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