Welcome to the LINCS PCCSE! 

WELCOME TO THE LINCS PCCSE PANORAMA REPOSITORY

This is the LINCS Proteomic Characterization Center for Signaling and Epigenetics (PCCSE) Panorama Repository for the reduced representation phosphoproteomics assay ("P100") and global chromatin profiling assay ("GCP") primary mass chromatogram data. Our center makes systematic perturbations (drug treatments, gene disruption/editing, and directed differentiation) in a variety of biological models including cancer and neurodevelopment. We read out molecular changes in the cells in the spaces of phosphosignaling (P100) and histone modification (GCP). In collaboration with the LINCS Center for Transcriptomics, we also read out changes in transcription using their L1000 assay. Look here for more information about our center or download our poster here.

PCCSE EXPERIMENTAL PARADIGMSANNOUNCING THE PCCSE PROTEOMICS CONNECTIVITY HUB
PCCSE Data Generation ParadigmsCLUE Proteomics Hub

Go beyond the heatmaps!  Explore connections and relationships among our perturbations in the Proteomics Connectivity Hub, a collaboration with the Connectivity Map Project.  Free account creation required.

NEW! ASMS 2017 Poster from our group!


LINCS PCCSE Data Quick Access Table 

Quick Links (Levels 1,2,4 data):

ALL P100 DATA ALL GCP DATA 

 

Quick Level 4 Data Visualization (& Download):

Note: this is probably what you want! For rapid access to visualizations of data, use the table below.  Clicking on any link will lead to a visualization of data that we have collected. Each cell is a plate ID number followed by links to the data where available.  Links beginning with "P" point to P100 data, while links beginning with "G" point to GCP data.  The numbers after the leading character describe length of compound treatment before samples were harvested.

 MCF7PC3A549A375YAPCNPCNeurons
Epigenetically-active drugs15 P3/G2418 P3/G2419 P3/G2417 P3/G2430 P3/G2416 P3/G24TBD
Neurodevelopmental drugs23 P3/G2424 P3/G2425 P3/G2422 P3/G2431 P3/G2420 P3/G24TBD
Kinase/Pathway Inhibitors29 P3/P6/P24/G2434 P3/G2433 P3/G2428 P3/G2432 P3/G2427 P3/G24TBD

Click here for more information on LINCS PCCSE Data Levels.

CUSTOM SUBSETTING OF

LEVEL 4 P100 DATA

CUSTOM SUBSETTING OF

LEVEL 4 GCP DATA


LINCS PCCSE Data Processing and Levels 

LINCS PCCSE Data Processing and Levels

LINCS espouses the concept of making different data levels available for public use.  Different data levels correspond different steps along our processing workflow.  The LINCS PCCSE levels are defined as follows:

Level 0 - Raw Mass Spectrometry Data (LCMS) - will be available through a chorusproject.org repository in the future

Level 1 - Probe Reads (SKY) - Curated Skyline documents; available on this website, including metadata

Level 2 - Raw Numerical Data (RPT) - Matrix data of extracted signal ratios of endogenous probes vs. internal standards; available on this website, including metadata

Level 3 - Normalized and QC'ed Numerical Data (QCNORM) - Matrix data derived from Level 2 after automated processing and normalization

Level 4 - Differential Quantification (DIFF) - Matrix data of Level 3 with plate-wide median ratio of each analyte subtracted from each sample; available on this website, including metadata 

These data levels are mapped onto our processing pipeline as depicted below:

TIP: To browse and access our data sets, hover over the "LINCS" folder in the upper left corner: