Downloads
This page hosts bulk downloads for all transcription factors in the UniPROBE database, organized by publication, and for the SQL tables holding PBM data or factor annotations. These files can be quite large, so please be prepared for significant download times. Please note that any files which contain PBM probe sequences are protected by an academic research use license, which will require confirmation prior to file download. Additionally, the various papers and datasets covered in this database have employed a variety of universal array designs created using various deBruijn sequences. Users interested in the 60mer probe sequences should download the probe sequences associated with the particular datasets or papers of interest.
If you wish to download individual files for certain transcriptions factors, you can find them most easily using the browse page, which provides an interface for textbased searches. The site's public directory index also makes all database files easily accessible.
All Data
Every download in this section contains a file for each protein in the database.
 Ungapped 8mer Data

The enrichment scores of the contiguous 8mers as calculated for each protein.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
 Normalized Probe Data (60mer signal intensities and sequences)

The median signal intensity values and corresponding nucleotide probe sequences.
 Raw Probe Data.

Text files containing the unprocessed output from the PBM array runs.
By Publication:
Liu et al., Cell, 2018
 All Data

This download includes all experimental data and computational analyses from Liu et al.'s compilation of Homo sapiens BCL11A and BCL11B PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each Mtf2_C factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Li et al., Nature, 2017
 All Data

This download includes all experimental data and computational analyses from Li et al.'s compilation of Homo sapiens Mtf2_C PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each Mtf2_C factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each Mtf2_C factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each Mtf2_C factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each Mtf2_C factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Mariani et al., TBD, 2017
 All Data

This download includes all experimental data and computational analyses from Mariani et al.'s compilation of PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each AP2 factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each AP2 factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each AP2 factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Santos et al., Cell Host Microbe, 2017
 All Data

This download includes all experimental data and computational analyses from Santos et al.'s compilation of Plasmodium falciparum PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Barrera et al., Science, 2016
 All Data

This download includes all eperimental data and computational analyses from Barrera et al.'s compilation of Homo sapiens PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each AP2 factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each AP2 factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each AP2 factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
LehtiShiu et al., Plant Physiology, 2015
 All Data

This download includes all experimental data and computational analyses from LehtiShiu et al.'s compilation of AP2 PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each AP2 factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each AP2 factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each AP2 factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each AP2 factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Lindemose et al, Nucleic Acids Res., 2014
 All Data

This download includes all experimental data and computational analyses from Lindemose et al's compilation of Arabidopsis thaliana PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Cheatle Jarvela et al., Molecular Biology and Evolution, 2014
 All Data

This download includes all experimental data and computational analyses from Cheatle Jarvela et al.'s compilation of Tbox PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each Tbox factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each Tbox factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each Tbox factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each Tbox factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Radke et al., PNAS, 2013
 All Data

This download includes all experimental data and computational analyses from Radke et al.'s compilation of Toxoplasma gondii AP2 (PF00847) PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each AP2 (PF00847) factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each AP2 (PF00847) factor: Download
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each AP2 (PF00847) factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each AP2 (PF00847) factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Soruco et al., Genes & Development, 2013
 All Data

This download includes all experimental data and computational analyses from Soruco et al.'s compilation of Drosophila melanogaster zfH2C2_2 PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each zfH2C2_2 factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each zfH2C2_2 factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each zfH2C2_2 factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each zfH2C2_2 factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Nakagawa et al., Proc Natl Acad Sci USA., 2013
 All Data

This download includes all experimental data and computational analyses from Nakagawa et al.'s compilation of Fork_head PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each Fork_head factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each Fork_head factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each Fork_head factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each Fork_head factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Peterson et al., Genes & Development, 2012
 All Data

This download includes all experimental data and computational analyses from Peterson et al.'s compilation of Mus musculus zfH2C2_2 PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each zfH2C2_2 factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each zfH2C2_2 factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each zfH2C2_2 factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each zfH2C2_2 factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Busser et al., PNAS, 2012
 All Data

This download includes all experimental data and computational analyses from Busser et al.'s compilation of Drosophila melanogaster Zinc Finger C2H2 PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each Zinc Finger C2H2 factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each Zinc Finger C2H2 factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each Zinc Finger C2H2 factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each Zinc Finger C2H2 factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Busser et al., Development, 2012
 All Data

This download includes all experimental data and computational analyses from Busser et al.'s compilation of Drosophila melanogaster Homeobox PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each Homeobox factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each Homeobox factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each Homeobox factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each Homeobox factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Helfer et al., Current Biology, 2011
 All Data

This download includes all experimental data and computational analyses from Helfer et al.'s compilation of Arabidopsis thaliana domain? PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each domain? factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each domain? factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each domain? factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each domain? factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
De Masi et al., Nucleic Acids Research, 2011
 All Data

This download includes all experimental data and computational analyses from De Masi et al.'s compilation of Caenorhabditis elegans bHLH PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each bHLH factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each bHLH factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each bHLH factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each bHLH factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Gordan et al., Genome Biology, 2011
 All Data

This download includes all experimental data and computational analyses from Gordan et al.'s compilation of Saccharomyces cerevisiae PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Del Bianco et al., PLoS ONE, 2010
 All Data

This download includes all experimental data and computational analyses from Del Bianco et al.'s compilation of Homo sapiens PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Alibes, et al., Nucleic Acids Research, 2010
 All Data

This download includes all experimental data and computational analyses from Alibes, et al.'s compilation of Homo sapiens PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each factor: Download
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each bHLH factor and dimer, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Wei, et al., The EMBO Journal, 2010
 All Data

This download includes all experimental data and computational analyses from Wei, et al.'s compilation of mus musculus ETS PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each ETS factor. The columns are as follows:
5 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
4: Median Intensity Signal
5: zscores calculated from the median SI data.
Separate files for each ETS factor: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each ETS factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Grove, De Masi et al., Cell 2009
 All Data

This download includes all experimental data and computational analyses from Grove, De Masi, et al's compilation of the C. elegans bHLH and dimers PBM results that are available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer for each bHLH factor and dimer. The columns are as follows:
3 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Enrichment score
Separate files for each bHLH factor and dimer: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a 0.25 threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor. Files ending in _RC.pwm contain the reverse complement of the forward PWM: Download
Single text file containing all PWMs: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices. Files ending in _RC.png show the logo for the reverse complement of the forward motif.
 60mer Probe Sequences

Holds separate text files for each bHLH factor and dimer, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Badis, Berger, Philippakis, Talukder, Gehrke, Jaeger, Chan, et al., Science 2009
 All Data

This download includes all experimental data and computational analyses from the most recent compilation of PBM results. These files include both raw and processed files from PBM array version 1 (v1) arrays, raw and processed files from array version 2 (v2) arrays, and the results of analyses performed to integrate the v1 and v2 array data. (Warning: this file is very large (~1.7GB) and may take several hours to download).
 All Ungapped 8mer Data

Median signal intensities, enrichment scores, zscores, pvalues for zscores, Qvalues for the enrichment scores, and Qvalues for the zscores associated with each contiguous 8mer. This file holds separate text files for each TF, where a given file has rows for each contiguous 8mer. The columns are as follows:
20 columns:
1: 8mer sequence
2: complement of 8mer sequence
3: Median Signal Intensity Version 1
4: Enrichment Score Version 1
5: ZScore (MAD estimation of sd) Version 1
6: Median Signal Intensity Version 2
7: Enrichment Score Version 2
8: ZScore (MAD estimation of sd) Version 2
9: Pvalue for ZScore Version 1
10: Pvalue for ZScore Version 2
11: Pvalue for combined ZScore from Array Versions 1 and 2
12: Pvalue for Enrichment Score Version 1
13: Pvalue for Enrichment Score Version 2
14: Pvalue for average Enrichment Score from Array Versions 1 and 2
15: FDR Qvalue for ZScore Version 1
16: FDR Qvalue for ZScore Version 2
17: FDR Qvalue for combined Zscores (ZScore Version 1, ZScore Version 2)
18: FDR Qvalue for Enrichment Score Version 1
19: FDR Qvalue for Enrichment Score Version 2
20: FDR Qvalue for averaged Enrichment Score from Array Versions 1 and 2: Download
Table of all median intensity values, array v1: Download
Table of all median intensity values, array v2: Download
Table of all enrichment scores, array v1: Download
Table of all enrichment scores, array v2: Download
Table of all enrichment scores, combined: Download
Table of all normalized zscores, array v1: Download
Table of all normalized zscores, array v2: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a specified threshold.
 PWMs

The position weight matrices (PWMs) for primary and secondary motifs. These files are in loglikelihood format, such that the value in each cell represents the frequency that a given nucleotide is predicted be present at the specified position.
Separate files for each factor: Download
Single text file containing all PWMs: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices.
 Raw Probe Data.

Text files containing the unprocessed output from the PBM array runs.
 60mer Probe Sequences

Holds separate text files for each TF, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences)
Lesch et al., Genes & Dev. 2009
 All Data

This download includes all experimental data and computational analyses from this publication that are included in UniPROBE.
 All 8mer Data

The median signal intensities and enrichment scores associated with each contiguous 8mer.
Single text file for all median intensities: Download
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Single text file containing all PWMs: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices.
 60mer Probe Sequences

Contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences).
Zhu, Byers, McCord, et al., Genome Research 2009
 All Data

This download is a compilation of all the yeast PBM experimental data and computational analyses available on UniPROBE. Please note that this file is very large (>.4GB) and may take several hours to download.
 All Ungapped 8mer Data

Median signal intensities and enrichment scores associated with each contiguous 8mer for each transcription factor. There are separate files for each transcription factor. The columns are as follows:
4 columns
1: 8mer sequence
2: Reverse complement of 8mer sequence
3: Median signal intensity
4: Enrichment score
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, zscores for the gapped 8mers with enrichment scores above a specified threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor: Download
Single text file containing all PWMs: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices.
 60mer Probe Sequences

Holds separate text files for each TF, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences).
Scharer et al., Cancer Res. 2009
 All Data

This download includes all experimental data and computational analyses from this publication that is available on UniPROBE.
 All 8mer Data

The median signal intensities and enrichment scores associated with each contiguous 8mer.
Single text file for all median intensity scores: Download
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Single text file containing all PWMs: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices.
 60mer Probe Sequences

Contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences).
Pompeani et al., Mol Microbiol 2008
 60mer Probe Sequences

The normalized signal intensities and nucleotide sequences of PBM probes (designed fom our 'all 10mer' de Bruijn sequences) for LuxR. There is no other factor data available from this publication.
Berger, Badis, Gehrke, Talukder, et al., Cell 2008
 All Data

This download includes all experimental data and computational analyses from the most recent compilation of the PBM homeodomain results that are available in UniPROBE. (Warning: this file is very large (~1.6GB)).
 All Ungapped 8mer Data

The enrichment scores, median signal intensities, zscores, pvalues for the enrichment, and Qvalues for the enrichment associated with each contiguous 8mer.
Separate files for each factor, where each file contains a column for each of the above statistics: Download
Single text file for all enrichment scores: Download
Single text file for all normalized intensity scores: Download
Single text file for all calculated zscores: Download
Single text file for all pvalues for enrichment: Download
Single text file for all Qvalues for enrichment: Download
Single text file for all Qvalues for the zscores: Download
 Top Gapped 8mer Data

Enrichment scores, median signal intensities, and zscores for the gapped 8mers with enrichment scores above a specified threshold.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor: Download
Single text file containing all PWMs: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices.
 Raw Probe Data.

Text files containing the unprocessed output from the PBM array runs.
 60mer Probe Sequences

Holds separate text files for each TF, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10mer' de Bruijn sequences).
De Silva et al., PNAS 2008
 All Data

This download includes all experimental data and computational analyses from this publication available in UniPROBE.
 All Ungapped 8mer Data

The median signal intensities and enrichment scores associated with each contiguous 8mer.
Separate files for each factor: Download
Single text file for all enrichment scores: Download
Single text file for all median intensity scores: Download
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor: Download
Single text file containing all PWMs: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices.
 Raw Probe Data.

Text files containing the unprocessed output from the PBM array runs.
Berger, Philippakis, et al., Nat. Biotech. 2006
 All Data

This download includes all experimental data and computational analyses from this publication that is available on UniPROBE.
 All Ungapped 8mer Data

The enrichment scores associated with each contiguous 8mer.
Separate files for each factor: Download
Single text file for all enrichment scores: Download
 Top Gapped 8mer Data

The enrichment scores for the gapped 8mers (up to 11 bp length) with enrichment scores above 0.25.
 PWMs

The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
Separate files for each factor: Download
Single text file containing all PWMs: Download
 Motif Logos

The motif logos derived from the corresponding position weight matrices.
 Raw Probe Data.

Text files containing the unprocessed output from the PBM array runs.
Separate files for each factor: Download
Excel spreadsheet containing raw data for all factors: Download
 60mer Probe Sequences

Microarry probes ranked by their normalized signal intensities (designed from our 'all 10mer' de Bruijn sequence).
Separate files for each factor: Download
Excel file containing data for all factors: Download
SQL Data: (Download)
Note: if you want to make use of the database SQL dump, you may need our functions to map kmers uniquely to and from integers, which is the form in which they are stored in the database. This file will provide you with the algorithm in the form of two different language implementations. Here is a UML diagram illustrating the relationships between the various tables in the database.