Datasets

1. Search is a very important part of this portal given that the number of LINCS datasets and precomputed signatures is constantly growing. One is able to search for a LINCS dataset and/or precomputed signature of interest on iLINCS portal in a couple of ways. In the example below, we will search for LINCS dataset for MCF7 cell line (the example of locating precomputed signature of interest is...

As seen in the figure below, clicking "Analyze" button next to any of the datasets, opens up a new window containing a landing page for that particular dataset. The figure above shows the landing page for the dataset with LINCS ID # EDS-1014. The typical dataset landing page layout contains a short dataset description, reference, exploratory tools and dataset analysis tools. On the bottom of the...

An experiment may have a number of samples which are organized in different groups (sample subgroupings). One may wish to restrict analysis to only a subset of all the available samples for an experiment. If you are interested in the analysis of differentially expressed genes between two groups of samples, you may create a two-group sample differential expression signature by clicking "Create...

"Create a signature" function generates a two-group sample differential expression signature within a selected dataset using top 100 differentially expressed genes between the groups as seen in the figure below. You may adjust the number of included genes for the signature creation. You can select a different set of differentially expressed genes based on different cutoff (fold change and p-values...

One may wish to restrict analysis to only a subset of all the available samples for an experiment. We have described earlier how to generate a two-group sample differential expression signature by clicking "Create a Signature". The following section will explain how to find differentially expressed genes between multiple groups of samples. 1. To find differentially expressed genes between multiple...