Published November 3, 2022
| Version v1
Journal article
Open
Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions
Authors/Creators
- 1. University of Parma
Description
Accompanying files to the manuscript "Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions" by Dembech et al.
The files enclosed here contain the full results of the co-transition (cotr) pipeline and the input files required to reproduce the results.
The code required to reproduce the results as well as python and R notebook to reproduce analyses and figures in the manuscript are available to the github repository: https://github.com/lab83bio/Cotransitions
Main files
================= FILES DESCRIPTION ================= Files Description -------------------------------------------------- ------------------------------------------------------------ Eukaryota.raxml.NL.transitions.annotated orthogroup pairs and scores (tab-separated) Eukaryota.raxml.LL.transitions.annotated orthogroup pairs and scores (tab-separated) Eukaryota.raxml.RL.transitions.annotated orthogroup pairs and scores (tab-separated) intersection.Eukaryota.raxml.RL.clusters mcl orthogroup clusters tab-separated (one cluster per line) intersection.Eukaryota.raxml.RL.clusters.annotated mcl clusters in human-readable format ============================================================= COLUMNS DESCRIPTION (Eukaryota.raxml.*.transitions.annotated) ============================================================= # Name Description --- ----------- ------------------------- 1 Orthogroup1 (Orthogroup1) 2 Orthogroup2 (Orthogroup2) 3 org (number of organisms) 4 t1 (Orthogroup1 transitions) 5 t2 (Orthogroup1 transitions) 6 c (concordant) 7 d (discordant) 8 k (concordant - discordant) 9 k_score (cotr score) 10 p (p-value) 11 p.adj (p-value adjusted)
Additional files
================= FILES DESCRIPTION ================= Files Description ------------------------------------------------------------------------- ----------------------------------------------------- Eukaryota.phylip.tree ncbi species tree in phylip format Eukaryota.phylip.data presence/absence data in phylip format Eukaryota.RData presence/absence tables in R data format RAxML_log.Eukaryota RAxML_result.Eukaryota RAxML_bestTree.Eukaryota RaxML fully resolved tree (phylip format) RAxML_info.Eukaryota Eukaryota.raxml.RL.nexus right-ladderized raxml tree in nexus format Eukaryota.raxml.LL.nexus left-ladderized raxml tree in nexus format Eukaryota.raxml.NL.nexus left-ladderized raxml tree in nexus format Eukaryota.raxml.RL.csv presence/absence table (tab-separated) with gene acc. Eukaryota.raxml.LL.csv presence/absence table (tab-separated) with gene acc. Eukaryota.raxml.NL.csv presence/absence table (tab-separated) with gene acc. Eukaryota.raxml.RL.csv.num_m gene numbers table (tab-separated) Eukaryota.raxml.LL.csv.num_m gene numbers table (tab-separated) Eukaryota.raxml.NL.csv.num_m gene numbers table (tab-separated) Eukaryota.raxml.RL.csv.num binary presence/absence table (tab-separated) Eukaryota.raxml.LL.csv.num binary presence/absence table (tab-separated) Eukaryota.raxml.NL.csv.num binary presence/absence table (tab-separated) Eukaryota.raxml.RL.transitions.annotated.odb.pickle orthogroup info from orthodb API Eukaryota.raxml.RL.transitions.annotated.unigo orthogroups mapped in Uniprot GO Eukaryota.raxml.RL.ogs.annotated.unigo.experimental.slim unigo file slimmed by owltools Eukaryota.raxml.RL.ogs.annotated.unigo.experimental.slim.boxcox.P.ranking slim file with normalized pvalues Eukaryota.raxml.RL.ogs.annotated.unigo.experimental.slim.boxcox.F.ranking slim file with normalized pvalues Eukaryota.raxml.RL.ogs.annotated.unigo.experimental.slim.boxcox.C.ranking slim file with normalized pvalues ============================================================= VARIABLES DESCRIPTION (Eukaryota.RData) ============================================================= # Name Description --- ------- --------------------------------------------------------------------------- 1 Gst Table with orthogroup genes in genomes 2 tr NCBI tree 3 Ngroups Genome table with GenomeID, number of orthogroups (N), TaxID, species names 4 cl_d data.table with taxonomic NCBI classification
Files
Eukaryota.raxml.LL.csv
Files
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