Difference between revisions of "Construct composite modules (analysis)"

Latest revision as of 18:14, 9 December 2020

Analysis title

Construct composite modules

Provider

geneXplain GmbH

Class

CMAAnalysis

Plugin

biouml.plugins.cma (Composite module analyst)

[edit] Description

Predicts composite module using the result of the "Site search on gene set" analysis. Composite modules - combinations of binding sites common for promoters of functionally related genes and responsible for the major component of the gene expression pattern of these genes. For more information see [1].

[edit] Parameters:

• Site search result – Result of previous site search run with background track
• Genetic algorithm parameters (expert) – Genetic algorithm parameters
  • Number of iterations – Number of iterations
  • Population size – Population size
  • Non-change limit – Number of iterations to stop after if best score is not improved
  • Elite size – Number of elite organisms (i.e. best organisms to survive unconditionally)
  • Mutation rate – This controls how often mutation occurs and how significant they are (0..1)
• Score calculation parameters (expert) – Parameters which control score calculation
  • Penalty rate – Which penalty value will be assigned
  • Site models in focus – At least one of these models must present in the resulting composite model to have non-zero score
  • Site models in focus table (expert) – The table of site models in focus
  • All modules contain site model in focus – If checked, then each module must contain at least one site model from the focus
  • Focused sequences percent – Minimal percent of sequences in yes-set which actually contains sites of site models in focus
  • Sequence column – Column to take sequences from
  • Sequences in focus – Selected sequences should be in the result top
  • Top sequences size (percent) – Size of sequences (in percent) that will be considered as top
  • Sequences in focus in top (percent) – Minimal percent of sequences in focus in the top
• Model parameters – Model parameters
  • Min modules – Minimal number of modules
  • Max modules – Maximal number of modules
  • Gaussian model (expert) – Gaussian model
    • Min models – Minimal number of site models in module
    • Max models – Maximal number of site models in module
    • Min sites to account – Minimal number of sites to account
    • Max sites to account – Maximal number of sites to account
    • Min module width – Minimal width (sigma) of the module
    • Max module width – Maximal width (sigma) of the module
    • Pairs mode – Whether the sites of at least two different site models satisfying the cut-off condition must be present on the sequence
• Output path – Path to store result

References:

1. Alexander Kel, Tatiana Konovalova, Tagir Valeev, Evgeny Cheremushkin, Olga Kel-Margoulis, Edgar Wingender. Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations. Bioinformatics. 2006 May 15; 22(10):1190-7. Epub 2006 Feb 10. doi: 10.1093/bioinformatics/btl041