Nomenclature and abbreviations

NM/refseq: Referense sequence collection (see NCBI refseq web page)

Unigene: Non-redundant set of gene-oriented clusters (see NCBI Unigene web page)

LocusLink: Single query curated interface (see NCBI LocusLink web page)

Position weight matrix (PWM): simple motif model where each position is assumed to be independent. Each entry in the matrix depends on the frequency of occurrence of each nucleotide at each position (see also Stormo and Fields 1998).

bp: base pair

kb: 1000 bp

TF: transcription factor

mm: Mus musculus

hs: Homo sapiens

dm: Drosophila melanogaster

sc: Saccharomyces Cerevisiae

List of IUPAC symbols for the nucleotides

Synergistic interactions results web page

- id1 id2 id3 id4: indices for the co-occurring motifs (click on motif to get more information)

- consensus m1 consensus m2 consensus m3 consensus m4: summary consensus sequence for the motif (scanning was performed using the weight matrix and not the consensus, though)

- ml1 ml2 ml3 ml4: motif length

- map1 map2 map3 map4: maximum a posteriori or motif identifier

- r_oc_sp1: normalized ratio of the number of occurrences in set to all genes

- r_tr_sp1: ratio of the number of transcript with the module to the total number of

- n_cooc_all: number of co-occurrences in all genes

- n_cooc_tr_all: number of genes with co-occurrences in all genes

- n_cooc_cl: number of co-occurrences in gene set

- n_cooc_tr_cl: number of genes with co-occurrences in gene set

- r_oc_sp1: n_cooc_cl/c_cooc_all normalized by the number of genes in each group

- r_tr_sp1: n_cooc_tr_cl/n_cooc_tr_all normalized by the number of genes in each group

p_binom: enrichment probability

n_files: number of different conditions in which the motif combination was found


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