Homo sapiens Comprehensive Model Collection (v9 - March 2012)

Website mirrors: autosome.ru, KAUST.

UPGMA clustering, pairwise similair computed by MACRO-APE at 0.0005 P-value; uniform PWM normalization; picture by jsPhyloSVG.
Then the motifs are arranged in clusters (shown in alternating colors) in a way that the minimal similarity between cluster members is 0.05.
Download the list of clusters, cluster logos, similarity matrix [xlsx], [txt].

We have used the high-performance motif discovery tool ChIPMunk to produce TFBS models for human TFs integrating data from different sources.
ChIPMunk was used in 4 different modes searching for optimal models in the lengths range from 7 to 22bp.
Then we manually selected the most reasonable models for each transcription factor and assigned the quality ratings from 'A' (best) to 'F' (fail).
The collection of 'A' to 'D' quality models represents the most reasonable subset to be used for further analysis.

The 'E'-part of the curated collection contains low confidence models.

The whole collection listing 4 models (f1,f2,si,do) for each TF.

• download the E part of the curated collection, small-BiSMark XML format, uniform background for PWMs
• download the E part of the curated collection, small-BiSMark XML format, hg19 background for PWMs
• download the E part of the curated collection, plain text format, weighted position count matrices (WPCM), rows as letters (ACGT)
• download the E part of the curated collection, plain text format, weighted position count matrices (WPCM), columns as letters (ACGT)
• download the E part of the curated collection, MEME text format, probability matrices
• download the E part of the curated collection, TRANSFAC text format, frequency matrices
• download the E part of the curated collection, plain text format, probability matrices, rows as letters (ACGT)
• download the E part of the curated collection, plain text format, probability matrices, columns as letters (ACGT)
• download the E part of the curated collection, plain text format, PWMs, uniform background, rows as letters (ACGT)
• download the E part of the curated collection, plain text format, PWMs, hg19 background, rows as letters (ACGT)
• download the E part of the curated collection, plain text format, PWMs, uniform background, columns as letters (ACGT)
• download the E part of the curated collection, plain text format, PWMs, hg19 background, columns as letters (ACGT)

• download the whole collection, small-BiSMark XML format, uniform background for PWMs
• download the whole collection, small-BiSMark XML format, hg19 background for PWMs
• download the whole collection, plain text format, weighted position count matrices (WPCM), rows as letters (ACGT)
• download the whole collection, plain text format, weighted position count matrices (WPCM), columns as letters (ACGT)
• download the whole collection, MEME text format, probability matrices
• download the whole collection, TRANSFAC text format, frequency matrices
• download the whole collection, plain text format, probability matrices, rows as letters (ACGT)
• download the whole collection, plain text format, probability matrices, columns as letters (ACGT)
• download the whole collection, plain text format, PWMs, uniform background, rows as letters (ACGT)
• download the whole collection, plain text format, PWMs, hg19 background, rows as letters (ACGT)
• download the whole collection, plain text format, PWMs, uniform background, columns as letters (ACGT)
• download the whole collection, plain text format, PWMs, hg19 background, columns as letters (ACGT)

[24 APR 2012] Improved visual representation for circular tree for HOCOMOCO-AC motifs.
[20 APR 2012] Circular tree for HOCOMOCO-AC motifs is available.
[10 APR 2012] UniProt mappings (HUMAN and MOUSE) for HOCOMOCO motifs are available for separate download.
[17 MAR 2012] HOCOMOCO v9 released. Many minor annotation fixes, downloads section updated.
[16 DEC 2011] E-collection list is now available online.
[15 DEC 2011] Complete separate model details pages for the HOCOMOCO-AD collection.
[14 DEC 2011] Precomputed thresholds for the HOCOMOCO-AD are available for download.
[13 DEC 2011] WPCM (weighted PCM) tag added to the small-BiSMark files. Downloads section updated.
[13 DEC 2011] Weighted PCMs are now available to download in the plain text format.