rRNA epitranscriptomic fingerprinting

Scripts used to analyze the sequencing data and build the figures used in Milenkovic et al., Mol Cell 2024 (accepted)

Table of Contents (to be edited)

• General Description
• Analysis of the Data
  • 1. Identification of differentially modified sites
  • 2. Validation of unannotated modification sites using Nano-CMC
  • 3. PCA and tissue classification based on dynamic rRNA modifications
  • 4. Identifying tumor-specific dynamic rRNA modifications and building tumor-aware Random Forest classifiers
• Dependencies and versions
• Citation
• Contact

General Description

The scripts used in the manuscript 'Epitranscriptomic fingerprinting reveals tissue-of-origin and tumor-specific signatures'

Analysis of the Data

The sequencing data produced in this work was analyzed using scripts listed in this github repository.

1. Identification of differentially modified sites

The script used to identify differentially modified sites across tissues and neuronal cells can be found in folders Figure_1 and Figure_2. Additional scripts, including the ones used for replicability analyses and outlier identification can be found in the folder Figure_S1-6.

2. Validation of unannotated modification sites using Nano-CMC

The scripts used to validate putative pseudouridylation sites are found in folder Figure_S8-9. For additional scripts refer to https://github.com/novoalab/yeast_RNA_Mod/tree/master/Analysis/NanoCMCSeq.

3. PCA and tissue classification based on dynamic rRNA modifications

The scripts used for PCAs and tissue-aware epitranscriptomic fingerprinting can be found in folders Figure_3 and Figure_S17.

4. Identifying tumor-specific dynamic rRNA modifications and building tumor-aware Random Forest classifiers

The scripts used for identifying tumor-specific dynamic rRNA modifications and building corresponding classifiers can be found in folder Figure_6 and Figure_S21.

Dependencies and versions

Software	Version
plyr	1.8.7
ggplot2	3.5.0
tidyverse	2.0.0
dplyr	1.1.2
ggrepel	0.9.3
MASS	7.3-53
ggpubr	0.6.0
tune	1.1.1
data.table	1.14.0
ComplexHeatmap	2.6.2
circlize	0.4.15
corrplot	0.93
gridExtra	2.3
ggforce	0.4.1
grid	4.0.3
klaR	1.7-1
psych	2.2.9
ggord	1.1.7
devtools	2.4.2
reshape	0.8.9
reshape2	1.4.4
randomForest	4.6-14
pROC	1.18.0

Citation

If you find this work/scripts useful, please cite:

Milenkovic I, Cruciani S, Llovera L, Lucas MC, Medina R, Pauli C, Heid D, Muley T, Schneider MA, Klotz LV, Allgauer M, Latuca R, LaFontaine LJ D, Muller-Tidow C and Novoa EM. Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures. Mol Cell 2024 (accepted). Preprint available: https://www.biorxiv.org/content/10.1101/2024.10.03.616461v1.full.pdf+html

Contact

Please open an issue in this repo if you encounter any difficulty running a script or have any doubts regarding the code. For correspondance, please contact [email protected].