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 60-mer 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 text-based 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 8-mer Data
-
The enrichment scores of the contiguous 8-mers as calculated for each protein.
- PWMs
-
The position weight matrices (PWMs) for each experiment. These matrices hold frequency values.
- Normalized Probe Data (60-mer 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each Mtf2_C factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each Mtf2_C factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each AP2 factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each AP2 factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' de Bruijn sequences)
Lehti-Shiu et al., Plant Physiology, 2015
- All Data
-
This download includes all experimental data and computational analyses from Lehti-Shiu et al.'s compilation of AP2 PBM results that are available on UniPROBE.
- All Ungapped 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each AP2 factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each AP2 factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 T-box PBM results that are available on UniPROBE.
- All Ungapped 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each T-box factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each T-box factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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 T-box 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.
- 60-mer Probe Sequences
-
Holds separate text files for each T-box factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each AP2 (PF00847) factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores 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.
- 60-mer 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 10-mer' 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 zf-H2C2_2 PBM results that are available on UniPROBE.
- All Ungapped 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each zf-H2C2_2 factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each zf-H2C2_2 factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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 zf-H2C2_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.
- 60-mer Probe Sequences
-
Holds separate text files for each zf-H2C2_2 factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each Fork_head factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each Fork_head factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 zf-H2C2_2 PBM results that are available on UniPROBE.
- All Ungapped 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each zf-H2C2_2 factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each zf-H2C2_2 factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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 zf-H2C2_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.
- 60-mer Probe Sequences
-
Holds separate text files for each zf-H2C2_2 factor, where a given file contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each Zinc Finger C2H2 factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each Zinc Finger C2H2 factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each Homeobox factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each Homeobox factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each domain? factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each domain? factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each bHLH factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each bHLH factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each ETS factor. The columns are as follows:
5 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
4: Median Intensity Signal
5: z-scores calculated from the median SI data.
Separate files for each ETS factor: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer for each bHLH factor and dimer. The columns are as follows:
3 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Enrichment score
Separate files for each bHLH factor and dimer: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
Median signal intensities, enrichment scores, z-scores, p-values for z-scores, Q-values for the enrichment scores, and Q-values for the z-scores associated with each contiguous 8-mer. This file holds separate text files for each TF, where a given file has rows for each contiguous 8-mer. The columns are as follows:
20 columns:
1: 8-mer sequence
2: complement of 8-mer sequence
3: Median Signal Intensity Version 1
4: Enrichment Score Version 1
5: Z-Score (MAD estimation of sd) Version 1
6: Median Signal Intensity Version 2
7: Enrichment Score Version 2
8: Z-Score (MAD estimation of sd) Version 2
9: P-value for Z-Score Version 1
10: P-value for Z-Score Version 2
11: P-value for combined Z-Score from Array Versions 1 and 2
12: P-value for Enrichment Score Version 1
13: P-value for Enrichment Score Version 2
14: P-value for average Enrichment Score from Array Versions 1 and 2
15: FDR Q-value for Z-Score Version 1
16: FDR Q-value for Z-Score Version 2
17: FDR Q-value for combined Z-scores (Z-Score Version 1, Z-Score Version 2)
18: FDR Q-value for Enrichment Score Version 1
19: FDR Q-value for Enrichment Score Version 2
20: FDR Q-value 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 z-scores, array v1: Download
Table of all normalized z-scores, array v2: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers with enrichment scores above a specified threshold.
- PWMs
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The position weight matrices (PWMs) for primary and secondary motifs. These files are in log-likelihood 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
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The motif logos derived from the corresponding position weight matrices.
- Raw Probe Data.
-
Text files containing the unprocessed output from the PBM array runs.
- 60-mer Probe Sequences
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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 10-mer' 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 8-mer Data
-
The median signal intensities and enrichment scores associated with each contiguous 8-mer.
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.
- 60-mer Probe Sequences
-
Contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10-mer' 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 8-mer Data
-
Median signal intensities and enrichment scores associated with each contiguous 8-mer for each transcription factor. There are separate files for each transcription factor. The columns are as follows:
4 columns
1: 8-mer sequence
2: Reverse complement of 8-mer sequence
3: Median signal intensity
4: Enrichment score
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The median signal intensities and enrichment scores associated with each contiguous 8-mer.
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.
- 60-mer Probe Sequences
-
Contains the normalized signal intensities and nucleotide sequences of PBM probes (designed from our 'all 10-mer' de Bruijn sequences).
Pompeani et al., Mol Microbiol 2008
- 60-mer Probe Sequences
-
The normalized signal intensities and nucleotide sequences of PBM probes (designed fom our 'all 10-mer' 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 8-mer Data
-
The enrichment scores, median signal intensities, z-scores, p-values for the enrichment, and Q-values for the enrichment associated with each contiguous 8-mer.
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 z-scores: Download
Single text file for all p-values for enrichment: Download
Single text file for all Q-values for enrichment: Download
Single text file for all Q-values for the z-scores: Download
- Top Gapped 8-mer Data
-
Enrichment scores, median signal intensities, and z-scores for the gapped 8-mers 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.
- 60-mer 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 10-mer' 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 8-mer Data
-
The median signal intensities and enrichment scores associated with each contiguous 8-mer.
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 8-mer Data
-
The enrichment scores associated with each contiguous 8-mer.
Separate files for each factor: Download
Single text file for all enrichment scores: Download
- Top Gapped 8-mer Data
-
The enrichment scores for the gapped 8-mers (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
- 60-mer Probe Sequences
-
Microarry probes ranked by their normalized signal intensities (designed from our 'all 10-mer' 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 k-mers 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.
