Search results for: cancer

Proteo-genomics analysis of cancer driver events in breast cancer (useCases)

Cancer Therapeutics Response Signatures (signatureLibraries)

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...

TCGA (datasets)

TCGA datasets are mRNA-seq data generated by The Cancer Genome Atlas project. The following cancers have been selected for study by TCGA because of their relatively poor prognosis and overall public health impact, as well as the availability of tumor and matched normal tissues that meet TCGA standards for patient consent, quality and quantity.

Use Cases (tutorialVideos)

Use case-1: Detecting and modulating mTOR pathway signaling. Use case-2: Proteo-genomics analysis of cancer driver events in breast cancer. Use case-3: Using iLINCS for analysis of transcriptional signature of COVID-19 infection.

GCP (assays)

Global Chromatin Profiling (GCP) technology is a mass spectrometry-based assay to identify and quantify post-translational modifications on histone proteins from bulk chromatin (i.e. measuring changes in epigenetic marks on histones). Around 60 different combinations of histone modifications can be quantified on H3, with even more possible combinations on H4, H2A (including isoforms), and H2B...

Reversing MTOR loss-of-function signature profile (useCases)

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...

Reversing Estrogen Receptor (ER) signature profile (useCases)

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...