Search results for: LINCS
The Library of Integrated Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents.
The LINCS Data and Signature Generation Centers produce a variety of data for the library. For such data to be standardized...
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...
The iLINCS (Integrative LINCS) portal facilitates interrogation of LINCS transcriptomic and proteomic datasets with user-defined gene lists. The workflow is as follows:
Paste a list of gene IDs (Entrez Gene IDs or HGNC approved symbols) or create one from a library of gene lists.
Select a LINCS or non-LINCS dataset for analysis
Perform statistical analysis of differential gene or protein...
The iLINCS (Integrative LINCS) portal is an web platform for analysis of LINCS data and signatures. The portal provides biologists-friendly user interfaces for analyzing transcriptomics and proteomics LINCS datasets. iLINCS web tools facilitate statistical analysis to identify differentially expressed genes and proteins; bioinformatics analysis to identify affected networks, pathway and gene lists...
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...
"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...
Signatures of perturbations assayed by P100 against 96 phosphopeptide probes and GCP assay against ~60 probes that monitor combinations of post-translational modifications on histones. The data is generated by using mass spectrometry techniques to characterize proteome level molecular signatures of responses to small molecule and genetic pertubations in a number of different cell lines.
iLINCS (Integrative LINCS) is an integrative web platform for analysis of LINCS data and signatures. The portal provides biologists-friendly user interfaces for analyzing transcriptomics and proteomics LINCS datasets. The portal integrates R analytical engine via several R tools for web-computing (rserve, opencpu, Shiny, rgl) and DCIC developed web tools and applications (FTreeView, Enrichr) into...
Transcriptional signatures of gene overexpression based on L1000 assay. The signatures consist of differential gene expressions and p-values for 978 Landmark Genes measured by L1000 assay. The signatures were created by aggregating (ie averaging) Level 4 data for biological replicates as defined by the signatures metadata. Only signatures designated to be reproducible and self-connected ("gold...
Transcriptional signatures of perturbations by small molecules based on L1000 assay. Signatures were created by aggregating (ie averaging) Level 4 data for biological replicates as defined by the signatures metadata. Only signatures designated to be reproducible and self-connected ("gold") by the Broad institute are represented. The signatures consist of differential gene expressions and p-values...
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...
Transcriptional signatures were constructed by further aggregating signatures of individual short hairpin RNA perturbations. The signatures are based only on the 978 Landmark Genes measured directly by the L1000 assay. The signatures for individual shRNA were created by aggregating (averaging) Level 4 data for biological replicates as defined by the signatures metadata. The signatures of...
Tutorial-1: iLINCS landing page Navigation.
Tutorial-2: Analyze my genes against LINCS datasets.
Tutorial-3: Analyze LINCS transcriptomic and proteomic datasets.
Tutorial-4: Analyze a drug signature and find other drugs with similar signatures.
Tutorial-5: Datasets workflow.
Tutorial-6: Signature workflow.
Tutorial-7: Genes workflow.
L1000CDS2 is an ultra-fast LINCS L1000 Characteristic Direction Signature Search Engine. (https://maayanlab.cloud/L1000CDS2/#/index)
216,105 transcriptional signatures of cellular perturbations constructed using the LINCS pilot phase L1000. The chemical perturbagen and individual shRNA signatures are created by aggregating (ie averaging) Level 4 data for biological replicates as defined by the signatures metadata. Only signatures designated to be reproducible and self-connected ("gold") by the Broad institute are represented...
Please visit:
iLINCS Workshop at LINCS Symposium Nov, 2020 and
Adverse Outcome Pathways with iLINCS - DEPHS Seminar for general workflows.
Alternatively you can go to iLINCS Video Portal for a complete set of tutorial videos.
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...
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 "Signatures" pipeline, you may explore, analyze and visualize over 200,000 pre-computed signatures (i.e. list of "scores" (activity levels) for a list of genes or for all genes in the genome "genome-wide signatures"). One would land on the Signatures landing page by clicking "Signatures" on the iLINCS portal header.
As shown in the figure above, there are 9 pre-computed signature libraries...
1. One may be interested to see all the metadata available for a particular precomputed signature. Let's say we would like to see more information for "LINCSCP_131839" signature. Let's click on the signature title as shown in the figure below.
2. As seen in the figure below, clicking on the signature title, opens up a new window containing a landing page for that particular signature. Similar...
The P100 assay is a mass spectrometry-based targeted phosphoproteomic assay that detects and quantifies a representative set of 96 phosphopeptide probes. Phosphopeptides are enriched via an automated protocol and then mixed with a set of isotopically-labeled internal standards that correspond to the analytes in the P100 assay. This mixture is introduced into a mass spectrometer using ultra-high...
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...
The iLINCS (Integrative LINCS) portal portal facilitates analysis of transcriptional drug signatures, and search for and analysis of groups of concordant transcriptional signatures of different drugs. The transcriptional signatures of chemical perturbagen activity in the iLINCS portal are constructed based on the Broad L1000 assay data. Each signature consists of the average z-scores and...
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...
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