Search results for: Proteomics
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.
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...
ToppFun: Transcriptome, ontology, phenotype, proteome, and pharmacome annotations based gene list functional enrichment analysis. (https://toppgene.cchmc.org/enrichment.jsp)
PiNET can be used to annotate, map and analyze a set of peptide moieties (including post-translationally modified peptides) identified by either targeted (SRM type) or SWATH (discovery) proteomic assays, or another related mass spectrometry based protein moieties identification and quantification technique. (http://pinet-server.org)
The transcriptomics or proteomics signature is constructed by comparing expression levels of
two groups of samples (treatment group and baseline group) using Empirical Bayes linear model
implemented in the limma package. For the GREIN collection of GEO RNA‐seq datasets, the
signatures are constructed using the negative‐binomial generalized linear model as implemented
in the edgeR package.
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.
Reverse-phase protein array (RPPA) is a high-throughput technology that performs protein assays on thousands of samples simultaneously that measure the levels of protein expression, as well as protein modifications such as phosphorylation. Protein lysates are arrayed as microspots on nitrocellulized coated glass slides and probed with highly specific antibodies that have been validated for RPPA...
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...
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...
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...
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...
GR calculator
GREIN
Signeta