Analysis of ribo-seq data:which measure to use when analyzing your

data?

Reut ShalgiRR Oct 14 2011

Global transcriptomics & proteomics data from 3T3 cells

Schwanha¨usser et al. Nature , May 2011

SILAC time course: 1.5h, 4.5h, 13.5h

prot. abundance (molec/cell)prot. syn. rates (molecules/(mRNA*h))prot ½ life (h)

mRNA synthesis labeling (4sU) for 2 hrs:

mRNA abundance (molec/cell)transcription rates (molecules/(cell*h))mRNA halflives (h)

Comparison with my 3T3 ribo-seq & RNA-seq data

Selbach mRNA copy num correlate with my RPKM

Selbach mRNA copy num vs prot copy num

my fp density vs. my RPKM

Comparison with my 3T3 ribo-seq & RNA-seq data

classical TE ANOTA TE

My recommendation:•best to use fp density to describe your data•don’t use TEs, not sure what they represent…