This page describes one module in the cisRED database, and is divided into three sections.

1. Module overview
   module size, module composition, and module discovery parameter settings.
2. Module details
   atomic motifs in this module, and a description and Gene Ontology (GO) information about the search regions which contain this module.
3. Definition of terms
   the types of objects contained in this database, and how these objects relate to each other.

Overview of module crmMmus642 (642 (Cdx-2__Nkx3-1))

Parameters used for module discovery
Maximum allowable annotation p-value	0.0004
Maximum allowable discovery p-value	0.005
Window width	300 bp
Minimum distance between motif starts	10 bp
Module must be found in at least this many search regions	10

The number of times a group name appears under the heading 'Groups in this module' indicates the number of motifs from that group that must participate in each instance of the module.

Module summary statistics
Module ID (crmMmus)	642
Module size	2-way
Groups in this module	crtMmus: 200451 (Nkx3-1)    200729 (Cdx-2)
Number of instances of this module	23
Number of search regions containing instances of this module	23
GO term FDR threshold	0.01
Total number of GO terms with FDR < threshold assigned to genes containing this module	10

This table ranks all the Gene Ontology (GO) terms for this module, based on their False Discovery Rate (FDR) for this particular module.
Terms that fail to meet the minimum FDR requirement of 0.01 do not appear in this listing.

GO term ranking
Rank	GO term	FDR	Number of genes in the GO database with this annotation	Number of genes in this module with this annotation
1	GO:0007154_cell_communication	0.0	537	19
2	GO:0007165_signal_transduction	0.0	520	19
3	GO:0007166_cell_surface_receptor_linked_signal_transduction	0.0	456	19
4	GO:0007186_G-protein_coupled_receptor_protein_signaling_pathway	0.0	411	19
5	GO:0007600_sensory_perception	0.0	383	18
6	GO:0007606_sensory_perception_of_chemical_stimulus	0.0	377	18
7	GO:0007608_sensory_perception_of_smell	0.0	370	18
8	GO:0050877_neurological_process	0.0	393	18
9	GO:0050896_response_to_stimulus	0.0	445	18
10	GO:0032501_multicellular_organismal_process	0.0012	589	18

Motifs in module crmMmus642 (642 (Cdx-2__Nkx3-1))

Each row in this table represents one instance of the module. Each instance is a set of atomic motifs which all appear within the same search region. Where available, functional information about the gene associated with each a promoter-based search region is also provided.

The numbers referenced in the 'GO terms' column below correspond to the GO term ranking shown in the preceeding table. If the gene used to create a promoter-based search region has been annotated with the GO term that was ranked N in the preceeding table, N will appear highlighted in the last column below.

Aside from viewing the module contents as presented here, you can:

• Click on a column heading to visit a page with information about that group.
• Click on a motif ID (in the first 2 columns) to visit a page with more information about that motif, including a list of all modules containing that motif.
• Click on a gene/region name to visit a page with more information about that search region, including a list of all modules found in that region.
• Click on one of the blue buttons located above the table to view a text file containing all the information shown in the table below, or just the names of all the search regions that contain this module.

Export Information from All 23 Regions

Export Only the Gene IDs from All 23 Regions

Definition of terms

Each cisRED database is based on a target genome, which is the genome of a target species, such as human, mouse, rat, or c.elegans.

The cisRED pipeline begins with the motif discovery stage, which operates on a large number of independent input sequence sets. An input sequence set consists of a sequence on the target genome, called the search region, and corresponding sequences from many other species. Search regions are generally 2-3k in size and are often located near a gene's transcription start site.

An atomic motif (or motif), is a set (or 'stack') of conserved sequences from some or all species of an input sequence set. A motif target sequence is the sequence that the target genome contributes to a motif. A motif can be represented by its sequence set/stack, or can be represented in a simplified form as a consensus sequence, a position frequency matrix, or a sequence logo.

A motif group (or group) is a set of similar motif target sequences. cisRED identifies groups using two different approaches: annotation and 'de novo'. Each motif group is labeled with a unique ID number. Currently, we consider annotation-based groups and modules to be more reliable than 'de novo' groups and modules. Work to improve genome-scale 'de novo' grouping is ongoing.

'De novo' groups of similar motif target sequences were identified by calculating edit distance dissimilarities between pairs of site sequences, for all significant site sequences, then hierarchically clustering the resulting similarity matrix using the OPTICS algorithm. An atomic motif is assigned to zero or one 'de novo' group.
Annotation-based groups of similar motif target sequences were identified by annotating against known site sequences (rather than against alignment matrices) in TRANSFAC, JASPAR, and ORegAnno. An atomic motif can belong to any number of annotation-based groups.

A module or pattern is a set of co-occuring motif group labels. A module is called either 'annotation-based' or 'de novo' depending on the type of groups it contains. (Currently, all groups in a module must be of the same type.) The size of a module is the number of co-occurring groups in that module. More precisely, a module may contain one or more references to a group label, and each group label reference counts towards the size of the group. A module of size N is called an N-way module.

A module instance (or pattern instance) is a list of motifs, all found in the same search region and in close proximity to each other, in which the motif target sequence of each motif in this list has been assigned to be in at least one of the module's group labels.

The module discovery process is based on a number of parameters, including the size of the 'window' (measured in bp), within which all the motifs in a module instance must be found, and the minimum number of search regions that must contain instances of the module.