This is a link to a summary of the MEME-ChIP results in an easy-to-parse "tab-separated values" format. Each line gives values for one motif found by MEME-ChIP. The fields are:

• MOTIF_INDEX -- The index of the motif in the "Motifs in MEME text format" file.
• MOTIF_SOURCE -- The name of the program that found the de novo motif, or the name of the motif file containing the known motif.
• MOTIF_ID -- The primary ID of the motif.
• ALT_ID -- The alternate ID of the motif.
• CONSENSUS -- The ID of the de novo motif, or a consensus sequence computed from the letter frequencies in the known motif (see below).
• WIDTH -- The width of the motif.
• SITES -- The number of sites reported by the de novo program, or the number of "Total Matches" reported by CentriMo.
• E-VALUE -- The statistical significance of the motif.
• E-VALUE_SOURCE -- The program that reported the E-value.
• MOST_SIMILAR_MOTIF -- The known motif most similar to this motif according to Tomtom.
• URL -- A link to a description of the most similar motif or to the known motif.

A consensus sequence is constructed from each column in a motif's frequency matrix using the "50% rule" as follows.

1. The letter frequencies in the column are sorted in decreasing order.
2. Letters with frequency less 50% of the maximum are discarded.
3. The letter used in this position in the consensus sequence is determined by the first rule below that applies:
• If there is only one letter left, or if the remaining letters exactly match an ambiguous symbol in the alphabet, the letter or ambiguous symbol, respectively, is used.
• Otherwise, if the remaining set contains at least 50% of the core symbols in the alphabet, the alphabet's wildcard (e.g., "N" for DNA or RNA, and "X" for protein) is used.
• Otherwise, the letter with the maximum frequency is used.

This is a link to a file containing all the significant motifs found by MEME-ChIP. The motifs are in MEME text format, and their IDs correspond to the motif indices given in the "Summary in TSV Format" file. Note:The "nsites=" and "E=" fields in the motif headers are only relevant for the MEME and DREME motifs. For known motifs, those values do not refer to the number of sites in the input sequences.

This is a link to the motif in the output of the particular motif discovery (e.g., MEME) or motif enrichment (e.g., CentriMo) program that reported it.

This is the significance of the motif according to the particular motif discovery (e.g., MEME) or motif enrichment (e.g., CentriMo) program that reported it.

Follow the link under the "Discovery/Enrichment Program" column for more information on how the significance value was derived.

Motifs reported by a motif discovery program (e.g., MEME) are compared with known motifs in a motif database specified by the user. This column lists the (up to) three most similar motifs. Only known motifs with TOMTOM similarity E-values of less than 1.0 to the discovered motif will be shown here. Clicking any of these links will show the TOMTOM results where all alignments can be viewed.

Motifs reported by a motif enrichment program (e.g., CentriMo) list the motif's name and a link to the motif's entry on the database website if it is available.

This graph shows the distribution of the best matches to the motif in the sequences as found by a CentriMo analysis.

The vertical line in the center of the graph corresponds to the center of the sequences.

Clicking on a motif's graph will take you to the CentriMo output with that motif selected for graphing.

Clicking here will show you all the motifs found by motif discovery or motif enrichment analysis that are significantly similar to the reported motif.

The additional motifs are shown aligned with the reported motif, sorted in order of significance of the motif according to the particular motif discovery (e.g., MEME) or motif enrichment (e.g., CentriMo) program that reported it.

To cluster the motifs MEME ChIP does the following:

1. Start with no groups and all significant reported motifs.
2. Run TOMTOM with all significant reported motifs to determine pairwise similarity.
3. Group Highly Similar Motifs---
   While ungrouped motifs:

   Select most significant ungrouped motif.

   This is called the "seed" motif for the group and we will call the E-value of its seed motif the group's "significance".

   Form a new group from the seed motif and all other motifs that are not yet in a group and who are strongly similar to the seed motif (default: TOMTOM E-value ≤ 0.05).
4. Merge Groups---
   For each group (most significant to least significant), merge it with any less significant group if all of its motifs are weakly similar to the first group's seed motif (default: TOMTOM E-value ≤ 0.1).

Clicking here takes you to the CentriMo motif enrichment analysis with the results for this all the motifs in this group.

This lists links to related content, which may include:

• Motif Spacing Analysis--SpaMo results using this motif as the "primary" motif, and each of the discovered motifs and motifs in any motif databases specified to MEME-ChIP as potential "secondary" motifs. SpaMo reports the secondary motifs whose occurrences are enriched at particular distances relative to the primary motif's occurrences in the input sequences.
• Motif Sites in GFF3--FIMO results showing the positions of occurrences of this motif in the input sequences in GFF3 format. If the input sequences to MEME-ChIP have FASTA headers following the UCSC style ("chromosome_name:starting_position-ending_position"), and the chromosome names are in UCSC (not ENSEMBL) format, the GFF3 output will be suitable for uploading to the UCSC Genome Browser as a custom track.