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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...
There is an extensive workflow in iLINCS API repository (https://github.com/uc-bd2k/ilincsAPI) to show how to embed iLINCS functionalities in R. This repository consists of set of examples to showcase the ways of interacting with iLINCS APIs.
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 a precomputed signatures for MCF7 cell line (the example of locating LINCS dataset of interest is...
In the following example, we will start with a gene knockdown (loss-of-function) transcriptional signature and will try to identify a drug or sets of drugs that have opposite transcriptional signatures. For this example, we will look at MTOR gene knockdown in PC3, prostate cancer cells; will compare its transcriptional signature to the known MTOR inhibitor drug, Sirolimus (Rapamycin) signature and...
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...
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...
1. One may also search for pre-computed signatures with pharmacological actions. To do this, let's click "Find Signatures with Pharmacological Actions" button on the bottom of Signatures pipeline landing page as shown below.
2. Clicking "Find Signatures with Pharmacological Actions" button will open a search field to input desired pharmacological actions as seen in the figure below. iLINCS will...
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...
"Genes" pipeline allows a query of genes of interest against LINCS data. One may start a query by inputing a list of genes via Entrez gene IDs or gene symbols separated by comma in the search field and clicking "Search for set of gene symbols or IDs". This section describes how to submit your own list of genes for analysis.
The figure above shows the screen to submit your own list of genes. You...
In the following example, we will try to identify a signature(s) that would reverse activated Estrogen receptor transcriptional signature profile. First, we will select Estradiol treatment perturbagen signature in MCF7 (ER+ breast cancer cell line) and then will identify highly disconnected (opposite) signature(s) to reverse its transcriptional signature profile via either gene loss-of-function...
In the following work-flow example, we will start with a prototypical drug and will identify sets of drugs that have similar transcriptional signatures. Moreover, we will also pinpoint genes and pathways that are affected by the drug.
1. First, let's open Signatures Pipeline starting with the iLINCS homepage as shown below.
2. This will take you to a Signatures pipeline landing page that lists...
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