3primeUTRproject

R/shell scripts related to 3' UTR project

Project body

R notebook

Main source code. They are split into two parts.

• tablePreparation.Rmd imports original tables, rearrange, modifies, and processes the table, then clusters gene expression data, perfroms GO-enrichment analyses, retrieves and separates 500bp upstream and downstream sequences into clusters.

• MotifOperations.Rmd performs MEME-discovery on clustered sequence files from the previous step, performs MAST (motif site counting) on MEME results, then compares discovered motifs to themselves and databases with TOMTOM. Then, gathers all results into motif table containing motif occurence data and gene expression.

• pipe-nodetail.Rmd sourcecode with less description

• 3primeRepo.Rproj an Rstudio project file.

BASH scripts

Part of MotifOperations.Rmd. Run in shell terminal outside of Rstudio.

• meme.sh A motif discovery tool. Finds motifs from input sequences.
• background_meme.sh performs MEME discovery on background sequences.
• mast.sh A motif site counter. Counts motif sites of input motifs from input sequences.
• meme2meme.sh A script for combining multiple meme result files into one file.
• tomtom.sh A motif comparison tool. Compares input motifs to input databases.

Materials

Sequence files

• materials_for_motif_operation.tar.gz contains clustered sequence files for starting MotifOperations.Rmd.

Tables

• materials_for_motif_operation.Rdata contains required tables for starting MotifOperations.Rmd.
• motif_table_dirty_group_added.txt motifs are manually grouped using spreadsheet and tomtom.html

backups for previous results reproduction

(See: MOTIF TABLES COMPARISON BETWEEN PREVIOUS RUN AND THE CURRENT RUN section in MotifOperations.Rmd)

• background_down_old.fasta:
• background_up_old.fasta:

Motif database for motif comparison

• GASCH_motif: motifs found from original paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC15070/)
• JASPAR2018_CORE_fungi_non-redundant_pfms_meme.txt: Motifs from JASPAR (transcription factor) db
• stab_motif: motifs related to RNA stability from https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-10-r86 motif source:https://webhome.weizmann.ac.il/home/tammyb/Shalgietal2005/
• subloc_motif: motifs related to sub-cellular localisation, same source as above.