Transcriptomes comparison through GO ranks.

Reproduced liver transcriptomes comparison from

Toren D, Kulaga A, Jethva M, Rubin E, Snezhkina AV, Kudryavtseva AV, Nowicki D, Tacutu R, Moskalev AA, Fraifeld VE. Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination. Aging Cell. 2020 [paper] [original code]

for 4 long-lived species:

• Bowhead whale, 211 years
• Gray whale, 77 years
• Brandt's bat, 41 years
• Naked Mole-Rat, 31 years

and 2 short-lived:

• Cow, 20 years
• Mouse, 4 years

Dependencies

• fastq-dump
• fastqc
• trimmomatic
• Trinity
• TransDecoder
• diamond
• salmon

Prepare data

• Create UniRef90 protein databases

  • wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/uniref/uniref90/uniref90.fasta.gz
  • run scripts/run_diamond_db.sh

• Prepare GO annotations

  • wget ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz

  • Filter with Mammalia taxons & Aspect(s)

    run python3 utils/prep_mammalia_goa.py

• Download RNA-seq data scripts/run_download.sh

Pipeline

• scripts/run_trimmomatic.sh
• scripts/run_quality.sh
• scripts/run_trinity.sh
• scripts/run_transdecoder.sh
• scripts/run_diamond.sh
• scripts/run_transdecoder.sh
• scripts/run_salmon_build.sh
• scripts/run_salmon.sh
• utils/process1.py
• utils/process2.py
• utils/process3.py

Create final heatmaps

• utils/heatmap_d.py
• utils/heatmap_u.py

Heatmaps

As a result, using only biological processes for ranking, I got the following heatmaps

DNA repair

Ubiquitination