Introduction to LINCS Content
From Array Suite Wiki
The LINCS project is an effort to investigate cellular responses to genetic and environmental perturbations, using cell lines as a model. OmicSoft's LINCS_B37 Land release provides analysis and visualization of expression and drug therapy responses for 115,209 samples and 359 unique treatments.
|Land Version||Genome Build||Gene Model|
Raw intensity measurements (LXB) are deconvoluted to provide intensity values for each landmark gene (the 978 directly measured features), producing the GEX data in the VALUE column of the sample data table. Log2-transformed raw fluorescence values (GEX data) is then normalized using a calibration curve based on invariant gene sets, and then quantile normalized. There are two sequential normalization steps: Luminex Invariant Set Normalization (LISS), and Quantile Normalization (QNORM). A model is applied to predict gene expression changes for a total of 22,268 features (INF_mlr12k column). Z-scores are then calculated for each feature with respect to a vehicle control population (ZSVCINF_mlr12k column) and also with respect to the population of all samples on the plate (ZSPVINF_mlr12k column).
The normalized signals (INF_mlr12k column) of landmark probeset (978) and imputed probeset (21,290) were used. Alv values were not renormalized. The signal is at log2 scale
Median values (INF_mlr12k column) are used for all summarizations; log2fc = median of (case - median of sample plate controls); P values are derived from standard distribution of median Z score(ZSVCINF_mlr12k) of all case samples.
LINCS Land has 115,209 samples and 28,234 comparisons, which consist of 359 unique treatments with various cell lines, dosages and treat time. The LINCS datasets encompass small molecules and genetic modifications that target multiple signaling pathways. To further cluster the treatments, we grouped the small molecules into the functional pathways and types of proteins they inhibit. When available, we added the protein target(s) of the small molecules to connect the small molecules that inhibit the same protein or the same signaling cascade. The 359 treatments have then been clustered to 21 treatment groups.