LINCS Workflow

Find proteomic and epigenomic data from the same conditions profiled by the L1000 assay

The LINCS Proteomic Characterization Center for Signaling and Epigenetics (PCCSE) generates small molecule perturbations for (i) epigenetic modulators; (ii) neurodevelopment and disease modulators and (iii) signaling pathway modulators.

The perturbations are assayed by P100, a targeted proteomic assay against 96 phosphopeptide probes that are commonly observed in diverse cell types; and GCP, a targeted proteomic assay against ~60 probes that monitor combinations of post-translational modifications on histones. The data is 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.

More information can be found at the LINCS PCCSE Panorama Repository. PCCSE signature datasets can be searched, downloaded and browsed with piLINCS. piLINCS can be used to interactively browse the different profiles generated, filtered based on cell - perturbation - dose tuples, merged across different profiles for the same tuples.

piLINCS Screenshot

iLINCS provides various analysis for the P100 datasets, it is possible to generate two-group sample differential expression signatures within a dataset, find differentially expressed proteins between multiple groups of samples, perform multi-group analysis for a specific protein list.

iLINCS Screenshot