Select rows below to plot only selected proteins
Unselect all or adjust typebox to reset
Select rows below to plot only selected proteins
Unselect all or adjust typebox to reset
Select rows below to plot only selected sites
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Select rows below to plot only selected sites
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Highlighted phospho-sites
Quantified phospho-sites in the meiotic timecourse dataset.
Select rows below to highlight selected phospho-sites
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Note this window only shows sites which were quantified as phosphorylated in our dataset. You may view the abundance profiles
of the same sites in the phospho-site dynamics window.
Motif search results
Find kinase motif sites in a protein.
Hover/click and scroll right to see full table.
Select rows below
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Note this window shows kinase motif sites in the selected proteins, across the full
ORF, but does not represent
bone fide
sites of phosphorylation as verified by MS. You may search for any protein in the SK1 proteome. Note the starting position of the motif is returned, which is not necessarily the putative phospho-acceptor residue.
Select a single row below
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Select a single row below
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Select a single row below
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Select a single row below
Unselect or adjust typebox to reset
This app was created to visualize results from our study. Please refer to our paper
for further information.
Phospho-proteomics was performed on samples of
Saccaromyces cerevisiae
undergoing
the meiotic divisions highly synchronously. All protein sequences are those for the SK1 strain background, retrieved
from
SGD
in 2019.
How to search
Type or select from the drop down menu proteins of interest. Use the buttons below the typebox
to choose whether you are searching for proteins by their common or systematic name. You may only search by one name-type at a time.
Typing or copy/paste returns names faster and not all names appear in the initial drop
down, even if they are found in the dataset, so it is best to type to search for them. If a protein name
does not appear when typed,
it was not included in our final dataset. You may select
multiple proteins together. To selectively delete names you have already entered, you may click to highlight
a name and press delete on your keyboard.
In all tabs, proteins or sites of interest can be selected from the results table that appears at the
bottom of the page, causing those selected to be plotted or highlighted in the main window. In the
spo13∆
tabs, only
one protein or phospho-site at a time can be selected for plotting.
How to explore and save the data
The plots and tables are mostly interactive, meaning hovering or clicking changes the visualization. For large tables,
you may hover/click and scroll right to see the rest of the table. You may save the plots
as a png by clicking the camera icon in the plot window or by clicking the download html button
to the right of the plot. You may sort the tables by clicking on the column headers. You may download the results
by clicking the Download Table buttons.
Abundance values
The abundance values shown are the average of two biological replicates of the meiotic divisions timecourse. Abundances have been normalized, batch-corrected, and are in a linear scale, see Methods of the paper for details.
Phospho-site abundances are all normalized to the corresponding total protein level. In the dynamics tabs, the abundance
of each protein or phospho-site was scaled to its mean value across all ten timepoints, which allows for comparison of dynamics between proteins/sites
with different baseline abundances. For WT vs
spo13∆
dynamics, each protein or site was scaled to the mean value of both WT and
spo13∆
timecourses (20 timepoints).
Phospho-site motifs
In this tab, the sequences of sites which were found to be phosphorylated in our dataset can be viewed. The sequence
shows the 31 amino-acid window around the central phospho-acceptor residue.
This means that the phospho-site is always amino acid 16 in the sequence. Underscores hold space for missing residues.
The kinase motif key at the bottom of the page indicates the patterns sites must possess to be called as matching
to each of the kinases. Amino acids within brackets are alternatives at that position, x represents any amino acid,
and the phospho-acceptor residue is starred. Note if the phospho-site sequence does not match any of the tested
kinase motifs shown in the key, the Kinase motif column is blank.
Kinase motif search
For discovery purposes, this tab allows users to search for kinase motif sites across the ORF of selected proteins. All motif matches in a given protein, including overlapping sites, of the 12 kinase motifs included in the study are returned. Note these do not represent
verified sites of phosphorylation and users should consult structural information available elsewhere to determine whether specific regions may be accessible to phosphorylation.
If the tested kinase motif is found in the protein, the kinase motif column says
true
. The total number of sites matching the selected kinase motif is found in the kinase motif number column and
the amino acid position of all motif matches is given in the kinase motif position column. The starting position of the motif is returned, which is not necessarily the putative phospho-acceptor residue. Note for downloading the results as a tsv, that if the list of positions is very long, that cell may not be displayed by MSExcel correctly.