Upload Signature File

One may also upload his/her signature file (fold change differential gene expression and p-values) to iLINCS portal and query it against the library of pre-computed signatures on iLINCS. To do this, let's click "Upload Signature File" located on the bottom of the Signatures pipeline landing page.

As seen in the figure below, you have the option to upload the Signature file to iLINCS portal (plain text, tab delimited files only - see sample file for an example) and select the library of pre-computed signatures that you would like to explore your signature file against. We'll select "LINCS chemical perturbagen signatures" library as an example.

As seen in the figure below, iLINCS portal will generate an uploaded signature page as soon as your submitted signature file is uploaded to iLINCS portal. iLINCS portal will by default select up to 100 top differentially expressed genes within the user uploaded signature (uploaded signature with less than 100 genes will be included in its entirety). You have the option to modify the number of included genes in your uploaded signature by using a Shiny Volcano plot by clicking "Modify the list of selected genes".

The generated uploaded signature page lists tools (such as EnrichR, L1000CDS2, etc.) that you may want to use to analyze your uploaded signature or, as seen in the figure below, you may proceed with connected (concordant) signatures analysis. To do this, you have to select a pre-computed signature library that you would like your uploaded signature to be compared against.

As seen in the screen-shot above, you may choose to include your complete uploaded signature (the example signature used has 10,000 genes) or select only few of the genes (the default top 100 genes or modified number of genes via Shiny Volcano plot). The numbers in gray oval shapes indicate the number of common genes between your uploaded signature and the signatures within a particular library. As an example, let's select "LINCS chemical perturbagen signatures" library using our complete uploaded signature and iLINCS portal will generate a list of Connected Signatures to your uploaded signature as seen in the figure below.

You may sort displayed signatures by concordance (pre-computed genome wide signatures which are positively or negatively correlated with the signature you have uploaded) and perform signature group analysis as it was described earlier.

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