Leoberium / uORF

Upstream Open Reading Frames

Regulatory Role of Upstream Open Reading Frames in RNA Degradation by Nonsense-Mediated Decay

Further ideas:

• Prepare new quantification of transcripts with StringTie or something similar
• Prior filtering of genes of with 1 exon, genes with long 3'UTRs, etc. Generally all groups of genes which may be confounding factors

Folders:

• diagnostic_plots_files and genes_plots_files are auxiliry folders with images for .Rmd files
• scripts - contains scripts with all preliminary data analysis
• vkr_scripts - scripts which were used for the preparation of thesis document
• UCSCHub - contains track and description files for UCSC Genome Browser Trackhub

Files:

• diagnostic_plots - boxplots and scatterplots of gene expression with different pseudocounts
• genes_plots - scatterplots of gene expression
• filtered_transcripts.tsv & transcripts_tsv & gene_table.tsv - tables of expression (including delta) of transcripts and genes with some metadata
• genes_vareps.tsv - table of gene expression and delta with different pseudocount
• msigdb_result.tsv - enrichment of upregulated genes
• positive_genes.txt - list of upregulated genes