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PlanTAMI

Tool for PLants Transcriptomes Analyisi with Mutual Information

This repository contains the most significant files generated during my thesis project

In addition to the source code of the tool is also available the wrapper for Galaxy,test data (Inflorescence transcriptome of Arabidopsis, Rice, Tomato and Barley) and a small collection of scripts used to handle and visualize data. For a detailed description of the tool and the dataset analysed refer to the file: Prototyping, implementation and validation of PlanTaMI.

This tool takes two lists of DEGs of different species and returns the direct orthologs and orthologs family enriched between the two set. To evaluate the family Normalise Pointwise Mutual Information is used and an empirical p-value is computed (bootstrapping).

The input needed by the tool are:

  • --plaza table with geneID, speciesID and familyID semicolon separed (https://bioinformatics.psb.ugent.be/plaza/)
  • --sp1 , --sp2 the species of DEGs (es. ath, sly, see plaza web site)
  • --in_sp1 --in_sp2 DEGs lists with the same nomenclature of the plaza table

The optional arguments are:

  • --th_sc the threshold for calling significant direct orthologs in the hypergeometric test (def=0.05)
  • --th the threshold for calling significant orthologs family corrected p-value in the NPMI analysis (def=0.05)
  • --random the number of list of rabndomID to compute empirical p-value (def=10000)
  • --FDR the method to adjust the p-value, Benjamini-Hochberg (BH) and Benjamini-Yekutieli (BY) are available (def=BY)
  • --sample the name of the sample to save results (def=my_sample_result)
  • --verbose the style of the output printed on the terminal during the run (0=none, 1=compact, 2=full, 3=line, def=1)

The output return by the tool are:

  • -significant_direct_orthologs (or NOT_significant_direct_orthologs) list of direct orthologs between the two species, the fold enrichment and the relative p-value

  • -significant_genes_sp1 list of gene IDs of sp1 resulted significant in the NPMI analysis

  • -significant_genes_sp2 list of gene IDs od sp2 resulted significant in the NPMI analysis

  • -significant_common_families_genes list of families significant in both sp1 and sp1 and the relative genes

  • -all_common_families_genes list of all families in common between sp1 and sp1 and the relative genes

  • -NPMI_results_sp1 table with NPMI value for each family of sp1 in common with sp2, in particulare are reported:

    • Fam_ID: Family ID
    • DEGs: DEGs in the family and family size
    • DEGs_set: DEGs in family of the same size in the input set
    • DEGs_genome: DEGs in family of the same size in the genome
    • p_my: DEGs in the set/DEGs in family of the same size in the set
    • p_all: (family size * DEGs in family of the same size in the set) / DEGs in family of the same size in the genome
    • npmi: log2(p_my/p_all)/-log2(p_all)
    • p_value: number of times i see higer or equal NPMI value in random set / number of set generated
    • FDR_bonf : Bonferroni multiple test correction
    • FDR_BY: Benjamini-Yekutieli (or Benjamini-Hochberg) multiple test correction

  • -NPMI_results_sp2 as above but for sp2

  • -stat feature of the backgroud, the sample and some easy to read results