What are my GENES doing in LINCS dataset?

You may interrogate gene and protein expression patterns in datasets and signatures for a selected set of genes of interest. In the example below, we are going to query a chosen set of genes in one of the LINCS datasets; we will interrogate MEP_LINCS RNA-seq dataset EDS-1014 for user-submitted list of genes of interest.

1. First, let's open Genes pipeline starting with the iLINCS homepage as shown below and input a list of genes of interest to be investigated and click "Search for set of gene symbols or IDs". For our example we will input CDK1, CDKN1A, CDKN2A, PCNA and AURKA into the search field.

2. Clicking "Search for set of gene symbols or IDs" will query iLINCS portal for the inputed genes as shown below. You may make any changes to found gene matches and submit the gene list to iLINCS by clicking "Analyze with 5 genes".

3. As shown in the figure below, iLINCS will perform query of your gene list in LINCS and non-LINCS datasets as well as over 200,000 pre-computed signatures. For our example, we will choose MEP_LINCS RNA-seq dataset EDS-1014 in the the list of LINCS datasets and will click "Analyze" to query our gene list in the chosen dataset. The Genes column shows number of genes found within a dataset from your gene list.

4. Clicking "Analyze" next to dataset of interest (EDS-1014 in our example), will query the selected dataset with the gene list that we have submitted earlier and will display a landing page for exploring and analyzing the selected dataset with your gene list. If you are interested in the analysis of differentially expressed genes between two groups of samples within a dataset, you may create a two-group sample differential expression signature by clicking "Create a Signature".

5. Clicking on the available analysis results tools will give you the option to further examine and explore the dataset with your selected gene list as shown in the figure below. You may also download publication-ready pictures for any of the displayed tool output.