Search results for: Transcriptomics
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)
RNA-seq is a Next Generation Sequencing platform that measures gene expression across the transcriptome. A population of RNA (total or fractionated, such as poly(A)+) is converted to a library of cDNA fragments with adaptors attached to one or both ends. Each molecule is then sequenced in a high-throughput manner to obtain short sequences from one end (single-end sequencing) or both ends (pair-end...
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 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.
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...
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...
These transcriptomic signatures were made using data from the Cancer Therapeutics Response Portal (CTRP) project. The data includes 860 cancer cell lines and combines basal (untreated) gene expression with measurements of sensitivity to 481 anti-cancer compounds. Drug sensitivity was measured as cell viability (ATP levels measured by CellTiter-Glo®) over a sixteen-point concentration-response...
GR calculator
GREIN
Signeta