Hypoxia associated modulation of the RNA-protein interactome in differentiated kidney tubular epithelial cells
Michael Ignarski, Constantin Rill, Rainer Kaiser, Madlen Kaldirim, René Neuhaus, Reza Esmaillie, Xinping Li, Corinna Klein, Katrin Bohl, Maike Petersen, Christian K. Frese, Martin Hoehne, Ilian Atanassov, Markus M. Rinschen, Katja Höpker, Bernhard Schermer, Thomas Benzing, Christoph Dieterich, Francesca Fabretti and Roman-Ulrich Müller## To whom correspondence should be addressed: Roman-Ulrich Müller, Dept. II of Internal Medicine, Kerpener Str. 62, 50937 Köln, roman-ulrich.mueller@uk-koeln.de.
Visualization of the supplemental table to Ignarski et al. 2018 is presented in 3 tabs:
- RBPome: Volcano plot for the RBPome in mIMCD3 cells under normoxic conditions.
- Proteome Normoxia: iBAQ ranks of proteins quantified in the mIMCD3 proteome (mean iBAQ over all samples).
- Proteome Hypoxia vs. Normoxia: Volcano plot of mIMCD3 proteome normoxia vs hypoxia (log2(foldchange) and -log10(p-value) of contrast hypoxia versus normoxia in proteome dataset) and correlation plot of RBPome in normoxic and hypoxic conditions.
On each of the three tabs the user can choose one of the following "modes":
- Mark one protein (choose one of the three options):
- Choose the gene name from the drop down menu. OR
- Type the gene name in the "Show a protein" field. OR
- Select a protein in the plot (left mouse click).
- Mark all class I proteins:
- Class I proteins are defined as RBPs that are significantly enriched (based on iBAQ intensities) in the crosslinked samples over non-crosslinked samples (t-test, FDR<0.1; s0=0.1) in either one of the three t-tests (total dataset, hypoxia, normoxia). Furthermore, all proteins, for which significance could not be calculated due to lacking detection in non-crosslinked samples (identification in ≤ 1 out of 6 replicates) despite clear presence after crosslinking (identification in ≥ 4 out of 6 replicates), were attributed to class I. 510 proteins fulfilled these criteria.
- Mark all class II proteins:
- Class II proteins are defined as proteins that were not significantly enriched but that had previously been identified to show RNA-binding capacity based on the recently published compendium, that includes 6 previously published datasets for Mus musculus and 6 for Homo sapiens (Hentze et al., 2018).
- Mark all novel RBPs:
- RNA-binding proteins are classified as novel RBPs as the 25 class I RBPs that have been identified in our RIC that have not been reported in previous screens of the mammalian RBPome.
Please note:
- The visualized values in the RBPome plot are based on the total dataset t-test. Consequently, proteins reaching significance in only hypoxic or normoxic condition may appear below significance threshold in this plot.
- More than one dot in plot for one gene name: Sometimes more than one measurement is assigned to one gene name. Usually these are cases with differing protein IDs (probably isoforms etc.) associated with one gene name (see data table).
- No dot assigned to a gene name in a plot: Some proteins are only measured in the proteome or in the RBPome. These proteins are missing in the respective other plot. The drop down menu contains all proteins.
- Proteins that are not measured at all in either -CL or +CL are not included in the plot. For these proteins please refer to the supplementary table.