Spike variant predictions

<p>Spike variant glycosylation predictions. (spike_mut_idx.v3.xlsx)</p> <p>&gt; Glycoimpact*: likelihood the glycosylation&nbsp;of a proximal site is perturbed&nbsp;</p> <p>&gt; mannoseDist*: aggregate Fisher&nbsp;log-OR for any high-mannose (&gt;5mannose) structure (taken from IMRs). LIkelihood high-mannose structures, in general, will increase or decrease</p> <p>&gt;&nbsp;IMR - Expected Change: a combination of proximity information with mannoseDist to estimate joint effect</p> <p>&gt; IMR/InSaNNE prediction: predictions of differential glycosylation from IMRs or InSaNNE respectively</p> <p>&nbsp;</p> <p>*_seq refers to sequence-based predictions, _str refers to structure-based predictions</p> <p>Generating R code is also provided without raw-data</p> <p>-----</p> <p>Update</p> <p>v4: Mannose/Complex column updated to Mannose/ Complex+hybrid in v5</p> <p>v5: Mannose+hybrid / Complex column added (one prediction changed). This column is more relevant to the validation MS observation.</p> <p>---</p> <p>Added 8/4/2021</p> <p>&gt; Results_untilGamma...xlsx</p> <p>Quantified using label-free analysis, which is semi-quantitative. We use precursor (peptide/MS1) peak area for quantitation, the spectral counts are also included. Peptide numbers, which give you the extent of sampling at each N-glycosylation site. We use Mean +/- SEM for the proportions of N-glycan variants (unoccupied, complex and high-mannose/hybrid).</p> <p>Other column headings should be self-explanatory, but please let me know if in doubt.</p> <p>The &ldquo;Result&rdquo; sheet is what you should look at. Other sheets are &ldquo;raw&rdquo; results. The first sheet &ldquo;Sequences&rdquo;, has all the sequence information. The color-coding is the regular one for N-glycans.</p>