{"action":"created","issue":{"url":"https://api.github.com/repos/dhimmel/opcendo/issues/1","repository_url":"https://api.github.com/repos/dhimmel/opcendo","labels_url":"https://api.github.com/repos/dhimmel/opcendo/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/dhimmel/opcendo/issues/1/comments","events_url":"https://api.github.com/repos/dhimmel/opcendo/issues/1/events","html_url":"https://github.com/dhimmel/opcendo/issues/1","id":137719898,"number":1,"title":"Compare interactions to microarray data from DA-cat mice","user":{"login":"dzoll","id":17558184,"avatar_url":"https://avatars.githubusercontent.com/u/17558184?v=3","gravatar_id":"","url":"https://api.github.com/users/dzoll","html_url":"https://github.com/dzoll","followers_url":"https://api.github.com/users/dzoll/followers","following_url":"https://api.github.com/users/dzoll/following{/other_user}","gists_url":"https://api.github.com/users/dzoll/gists{/gist_id}","starred_url":"https://api.github.com/users/dzoll/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dzoll/subscriptions","organizations_url":"https://api.github.com/users/dzoll/orgs","repos_url":"https://api.github.com/users/dzoll/repos","events_url":"https://api.github.com/users/dzoll/events{/privacy}","received_events_url":"https://api.github.com/users/dzoll/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-03-01T23:27:06Z","updated_at":"2016-03-02T02:32:03Z","closed_at":null,"body":"I would like to search for potential interaction pairs identified in \"interactions\" in an other database from a microarray study. The attached file is a list of genes deferentially expressed in 4 day old Dominant Active-catenin mice which exhibit upregulated Wnt signalling specifically in OPCs.  Citation: Fancy et al., 2011 Nat Neurosci, doi: 10.1038/nn.2855\r\n\r\nraw data source: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19403\r\n\r\n[ClassComparisonP4.xlsx](https://github.com/dhimmel/opcendo/files/153794/ClassComparisonP4.xlsx)\r\n"},"comment":{"url":"https://api.github.com/repos/dhimmel/opcendo/issues/comments/191022298","html_url":"https://github.com/dhimmel/opcendo/issues/1#issuecomment-191022298","issue_url":"https://api.github.com/repos/dhimmel/opcendo/issues/1","id":191022298,"user":{"login":"dhimmel","id":1117703,"avatar_url":"https://avatars.githubusercontent.com/u/1117703?v=3","gravatar_id":"","url":"https://api.github.com/users/dhimmel","html_url":"https://github.com/dhimmel","followers_url":"https://api.github.com/users/dhimmel/followers","following_url":"https://api.github.com/users/dhimmel/following{/other_user}","gists_url":"https://api.github.com/users/dhimmel/gists{/gist_id}","starred_url":"https://api.github.com/users/dhimmel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dhimmel/subscriptions","organizations_url":"https://api.github.com/users/dhimmel/orgs","repos_url":"https://api.github.com/users/dhimmel/repos","events_url":"https://api.github.com/users/dhimmel/events{/privacy}","received_events_url":"https://api.github.com/users/dhimmel/received_events","type":"User","site_admin":false},"created_at":"2016-03-02T02:32:03Z","updated_at":"2016-03-02T02:32:03Z","body":"I added this dataset and reran the analysis. I didn't apply any filters, but added the fold changes to the data files for inspection.\r\n\r\n> DA Cat fc? As in dominant active catenin fold change\r\n\r\nOkay I named the column `DA_Cat_fold_change` or `dac_fc` for short.\r\n\r\n## Data provenance\r\n\r\n@dzoll provided a processed version of GSE19403 [above](#issue-137719898) named  `ClassComparisonP4.xlsx`. We didn't use this version, since it was affected by the [Excel gene-to-date bug](https://doi.org/10.1186/1471-2105-5-80 \"Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics\"). However, this Excel file was exported from an html document. GitHub did not allow @dzoll to attach this html file, but he emailed it to me. I extracted the table as a text file, available at [`download/dominant-active-catenin-DEGs.tsv`](https://github.com/dhimmel/opcendo/blob/8f20c49dbbc17767b8d5ed46f5c094b700306ce1/download/dominant-active-catenin-DEGs.tsv)."}}