Search results for: L1000
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...
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...
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...
L1000CDS2 is an ultra-fast LINCS L1000 Characteristic Direction Signature Search Engine. (https://maayanlab.cloud/L1000CDS2/#/index)
L1000 fireworks display (L1000FWD) is a web application that provides interactive visualization of over 16000 drug and small-molecule induced gene expression signatures. (https://maayanlab.cloud/L1000FWD/)
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...
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...
The perturbagen connectivity analysis compares the query signature to all signatures
for a given perturbagen as a group, thus extending the pair-wise connectivity analysis
to account for diversity of responses in different cellular contexts. This
is accomplished by performing the enrichment analysis of individual connectivity
scores between the query signature and set of all L1000 signatures of a...
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...
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...
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...
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