klmr / thesis

My PhD thesis, “Investigating the link between tRNA and mRNA abundance in mammals”

PhD thesis manuscript

Download the final version. This is the version that was deposited with the University of Cambridge in digital and hardbound form.

How to build

# This won’t actually work unless you magically have the same library as I.
make references.bib
make thesis

Requirements

• My reference library.
• Fonts:
  • TeX Gyre Pagella
  • Gill Sans
  • WenQuanYi Zen Hei Mono

thesis's Issues

PCA of mean GO term codon usage

How did you perform this? "PCA of mean GO term codon usage" I was reading your thesis saw in this chapter

Implications of codon–anticodon interaction on the regulation of translation

Can i use for differential analysed genes on which I ran gene ontology now I have the ontology. can you show me a dummy example how to perform this.

I have done PCA on expression and sample wise but not like this. I would like to do the same.

Any suggestion or help would be highly appreciated

How are you defining gene/transcript expression?

In rna-seq.tex you have excellent discussion of various aspects of expression quantification. I think there are some missing pieces:

• Given that you state you are interested in transcript quantification, how do you actually quantify transcripts? Mapping to genomic features does not provide this because of shared exons, so how are you getting transcript abundance measures? And how do you handle multi-mapping reads?
• In several places you mention gene expression. How are you defining this? If the molecule of interest is the transcript, how is gene expression defined relative to expression of each transcript?
• RPKM is unstable across samples by definition because the normalisation factor is sample-specific. This is not the case for TPM, which is only unstable due to the molecular population makeup instability that you mention.