Construct composite modules (analysis)

Analysis title

Construct composite modules

Provider

geneXplain GmbH

Class

CMAAnalysis

Plugin

biouml.plugins.cma (Composite module analyst)

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].

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