Bench
Cell and tissue culture
Molecular biology
Cell-based assays
In vivo
PDX is a patient-derived xenograft, a mouse carrying tumor tissue taken from a patient. CDX is a cell line-derived xenograft, a mouse carrying tumor cells grown in the lab.
Data and public resources
Data types
Repositories and reference sets
TCGA is The Cancer Genome Atlas and CGGA is the Chinese Glioma Genome Atlas, both public collections of molecular data from patient tumors. Ivy GAP is an atlas of glioblastoma measurements labeled by where in the tumor they were taken. CPTAC is a public proteomics resource. GEO is the Gene Expression Omnibus.
Bulk RNA-seq
Differential expression asks which genes change between two groups of samples. Kaplan-Meier and Cox regression relate those changes to how long patients survive.
Single-cell RNA-seq
Single-cell RNA-seq measures gene activity one cell at a time, so a signal can be traced to the cell type producing it rather than to the tumor as a whole.
Signature scoring and enrichment
A gene signature is a defined set of genes that stand for one biological program. Scoring measures how strongly that program is switched on in a sample or in a single cell.
Tumor composition
Deconvolution estimates which cell types make up a bulk tumor sample, and in what proportion, from a single mixed measurement.
Statistics and networks
WGCNA groups genes that rise and fall together across samples, which finds programs without being told what to look for.
Software and languages
R
Python
Other languages
Statistics and figures
Networks, structure and platforms
I-TASSER, SWISS-MODEL and PHYRE2 predict the three-dimensional shape of a protein from its sequence. Gephi draws and analyzes networks. TISON is the multi-scale cancer modeling platform described on the research page.