Profile types

This Wiki page is a part of piLINCS quick help.

At present, piLINCS enables access to the reduced representation phosphoproteomic ("P100") and global chromatin ("GCP") profiles generated by using mass spectrometry techniques to characterize proteome level molecular signatures of (responses to) small molecule and genetic perturbations in a number of different cell lines (for details see LINCS/Broad). These different profiles are obtained by merging QC+NORM level processed GCT files from Panorama repository, and subsequently processed further to create various 'views' of such obtained overall data set to facilitate its use by the community.

These 'views', or types of profiles that can be accessed and exported through piLINCS are as follows:

• Raw data: high level data from Panorama with individual measurements using the QC+NORM normalization
• Profiles: data reorganized as actual profiles with individual replicates
• Merged profiles: data reorganized as merged/collapsed profiles with replicates collapsed into averaged profiles

In order to explore these different options while browsing data interactively, one can use the corresponding tabs:

• Raw data tab,
• Profiles tab
• Merged profiles tab

These three different levels/types of profiles are also used to export data under the Export tab.

Note that merged profiles can also be used to display (and export) joint (concatenated) P100+GCP profiles that effectively provide a more global view of proteomic responses to genetic and/or chemical perturbations across different subspaces/readouts. Concatenation of P100 and GCP takes places at the level of average profiles with technical replicates for any given tuple collapsed.

Note that 'Merged profiles' with both P100 and GCP profiles to be concatenated require that both are available for any given tuple (cell type, perturbation, dose, time). Only the existing part of the joint profile will be shown, if data is available for only one of those profile.