Kreiman Lab

List of parameters to the program

input_filename = list with ids of potentially co-regulated genes
search_type = type of identifiers in the input_filename ('ll' = LocusLink, 'nm' = Refseq, 'ug' = Unigene, 'cg' = flybase, 'ens' = ensembl, 'affy' = Affymetrix) [default = 'll']
experiment_name = experiment name
experiment_id = experiment id (allows to run multiple different parameters for a given experiment name)
species1 = first species (hs=Homo sapiens, mm=Mus musculus, dm=Drosophila melanogaster, sc=Saccharomices cerevisiae) [default = 'hs']
species2 = second species (set to 'none' to skip across species comparisons) [default = 'mm']

max_ul_length = maximum upstream length [default = 5000 bp]
max_exon1_length = maximum exon length (set to 0 to skip exon) [default = 5000 bp]
max_intron1_length = maximum intron length (set to 0 to skip exon) [default = 5000 bp]
motif_comparison_threshold = threshold correlation coefficient to consider two motifs redundant (range = [-1,1]; default=0.7; set to 1 to consider all motifs to be distinct)
rc = 1 to consider both strands and 0 to consider only the + strand (default = 1)
threshold_type = type of threshold used in motif scanning ('min_fp' = minimize false positives; 'min_fn' = minimize false negatives; default = 'min_fn')
min_dist_factor = minimum distance between adjacent motifs (min_distance = min_dist_factor * motif_length; default = 0.5)

mask_nonconserved = 1 to mask non-conserved sequences (only valid if species2 not equal to 'none'; default = 1)
include_noorth = 1 to include genes for which no orthologous gene is available (only valid if species2 not equal to 'none and mask_nonconserved = 1; default = 0)
source = 'gbk' for genbank sequences, 'ensembl' for ensembl sequences, 'sgd' for Saccharomyces genome databse

max_dist = maximum distance between motifs (default = 100 bp)
order_constraint = 1 to consider the order of motifs within a module and 0 otherwise (default = 0)
minian = minimum number of genes in which the module must be present (default = 4)
locuslink_only = 1 to restrict the whole genome search to valid LocusLink entries (this only applies to hs or mm cases, default = 1)
p = p value threshold for the enrichment criterion (default = 0.001)

process_alignace = 1 to run alignACE motif search program (default = 1)
process_motifsampler = 1 to run motifSampler motif search program (default = 1)
process_meme = 1 to run MEME motif search program (default = 1)
include_transfac = 1 to include the TRANSFAC motifs for species1 (and species2; default = 1)
information_threshold = average motif information_threshold (range = [0,2]; default = 0.4)
seq_variety_threshold = motif variety threshold (range = [0,4]; set to 0 to disregard this constraint; default = 1)
n_seqs_threshold = minimum number of sequences used to define a motif (default = 6)
min_motif_length_threshold = minimu motif length (default = 6)
max_motif_length_threshold = maximum motif length (default = 30)

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