Purpose

To focus our investigation of omega-3 metabolism, we are compiling a list of relevant genes. As a start, we selected 19 KEGG pathways, but eventually we might also include pathways from other databases. Unfortunately, the KEGG pathways include only enzymes, not regulators or transporters (SREBP, LXR, FABP’s etc.), so we’ll have to add the latter manually.

The gene list below is a large, autogenerated table showing

Now we’d like your help in adding notes to this list, and to make it both shorter and more complete. Thus:

Notetaking will happen in a shared spreadsheet: If you click the “yes” or “no” in the “note” column of the gene list, you will be taken to an Excel-like Google sheet. Also, the “add new gene” button below opens the same Google sheet. What we need you to do is fill in whatever identifier you have for the gene, and a literature reference, and a freetext comment. The “note” column of the gene list says “yes” if we’ve made any notes, in which case you can mouse over the text “yes” and see our notes. We will regenerate the gene list periodically to update this column.

This document is very JavaScript-heavy, so will take a while to load. Once loaded, the list can be sorted by column (click the headers) and filtered (search box top right of the table). The table is responsive, meaning that it will display as many columns as there is room for. The remaining data for a given record can be expanded by clicking the green plus sign in that row. The columns “orthogroup.plot” and “clan.plot” link to figures of gene trees. All links will open in new tabs, to avoid having to reload or re-render this document.

Pathways

We wish to connect KEGG’s representation of these to the Atlantic salmon genome, and to the ZebraGEM genome-scale metabolic reconstruction for zebrafish (MODEL1204120000).

Our KEGG pathways of interest

Manual search of kegg.pathway found these:

id name map ko ec rn dre
00010 glycolysis / gluconeogenesis map00010 ko00010 ec00010 rn00010 dre00010
00030 pentose phosphate pathway map00030 ko00030 ec00030 rn00030 dre00030
00061 fatty acid biosynthesis map00061 ko00061 ec00061 rn00061 dre00061
00062 fatty acid elongation map00062 ko00062 ec00062 rn00062 dre00062
00100 steroid biosynthesis map00100 ko00100 ec00100 rn00100 dre00100
00120 primary bile acid biosynthesis map00120 ko00120 ec00120 rn00120 dre00120
00140 steroid hormone biosynthesis map00140 ko00140 ec00140 rn00140 dre00140
00561 glycerolipid metabolism map00561 ko00561 ec00561 rn00561 dre00561
00564 glycerophospholipid metabolism map00564 ko00564 ec00564 rn00564 dre00564
00600 sphingolipid metabolism map00600 ko00600 ec00600 rn00600 dre00600
00900 terpenoid backbone biosynthesis map00900 ko00900 ec00900 rn00900 dre00900
01040 biosynthesis of unsaturated fatty acids map01040 ko01040 ec01040 rn01040 dre01040
01212 fatty acid metabolism map01212 ko01212 ec01212 rn01212 dre01212
02010 abc transporters map02010 ko02010 ec02010 rn02010 dre02010
03320 PPAR signaling pathway map03320 ko03320 ec03320 rn03320 dre03320
04070 phosphatidylinositol signaling system map04070 ko04070 ec04070 rn04070 dre04070
04910 insulin signaling pathway map04910 ko04910 ec04910 rn04910 dre04910
04975 fat digestion and absorption map04975 ko04975 ec04975 rn04975 dre04975
04976 bile secretion map04976 ko04976 ec04976 rn04976 dre04976

Terpenoid backbone biosynthesis (which includes the mevalonate pathway) is included because it leads to steroid biosynthesis.