GEO DataSets

(Submitter supplied) Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by array

Platform:

GPL23305

4 Samples

Download data: TXT, XLSX

(Submitter supplied) Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by array

Platform:

GPL23935

2 Samples

Download data: TXT

(Submitter supplied) Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by array

Platform:

GPL23935

3 Samples

Download data: TXT

(Submitter supplied) Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by array

Platform:

GPL23935

3 Samples

Download data: TXT

(Submitter supplied) Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL23935

3 Samples

Download data: TXT

(Submitter supplied) Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. more...

Organism:

synthetic construct; Homo sapiens

Type:

Other

Platform:

GPL19244

5 Samples

Download data: TXT, XLSX

(Submitter supplied) Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL17173

4 Samples

Download data: TXT, XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; synthetic construct

Type:

Genome binding/occupancy profiling by array

5 related Platforms

28 Samples

Download data: TXT

(Submitter supplied) Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by array

Platform:

GPL23293

4 Samples

Download data: TXT, XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Protein profiling by protein array

Platforms:

GPL16704 GPL16703

5 Samples

Download data: TXT

(Submitter supplied) DNA sequence is a major determinant of the binding specificity of transcription factors (TFs) for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with highly similar DNA binding motifs but distinct in vivo targets. Currently, it is not well understood how TFs with seemingly identical DNA motifs achieve unique specificities in vivo. Here, we used custom protein binding microarrays to analyze TF specificity for putative binding sites in their genomic sequence context. more...

Organism:

Saccharomyces cerevisiae

Type:

Protein profiling by protein array

Platform:

GPL16704

2 Samples

Download data: TXT

(Submitter supplied) DNA sequence is a major determinant of the binding specificity of transcription factors (TFs) for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with highly similar DNA binding motifs but distinct in vivo targets. Currently, it is not well understood how TFs with seemingly identical DNA motifs achieve unique specificities in vivo. Here, we used custom protein binding microarrays to analyze TF specificity for putative binding sites in their genomic sequence context. more...

Organism:

Saccharomyces cerevisiae

Type:

Protein profiling by protein array

Platform:

GPL16703

3 Samples

Download data: TXT

(Submitter supplied) Development of the human malaria parasite, Plasmodium falciparum is regulated by a limited number of sequence-specific transcription factors (TFs). However, the mechanisms by which these TFs recognize genome-wide binding sites to regulate target genes is still largely unknown. To address TF target specificity, we investigated the binding of two TF subsets that either bind CACACA or GTGCAC and further characterized PfAP2-G and PfAP2-EXP which bind unique DNA motifs (GTAC and TGCATGCA). more...

Organism:

Plasmodium falciparum

Type:

Other

Platform:

GPL33273

12 Samples

Download data: GPR, TXT

(Submitter supplied) Global transcription of the malaria parasite, Plasmodium falciparum, is finely regulated, yet the genome encodes for a limited number of sequence-specific transcription factors (TFs) to coordinate this pattern. A subset of these TFs bind overlapping DNA motifs (i.e., CACACA and GTGCAC); however, mechanisms of binding site selection and redundancy have not yet been investigated in P. falciparum. Therefore, we integrated a variety of approaches from new and published work such as high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post translational modification mapping, and genome-wide chromatin accessibility mapping to comprehensively interrogate the impact of DNA sequence context and the chromatin landscape on TF binding in P. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL32020 GPL21078

8 Samples

Download data: BED, BIGWIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae; synthetic construct

Type:

Other

Platform:

GPL29513

22 Samples

Download data: TXT

(Submitter supplied) Most eukaryotic transcription factors (TFs) are part of large protein families, with members of the same family (i.e. paralogous TFs) recognizing similar DNA-binding motifs but performing different regulatory functions. Many TF paralogs are co-expressed in the cell, and thus can compete for target sites across the genome. Here, we show that direct competition for DNA binding between TF paralogs is a major determinant of their genomic binding patterns. more...

Organism:

synthetic construct; Saccharomyces cerevisiae

Type:

Other

Platform:

GPL29513

8 Samples

Download data: TXT

(Submitter supplied) Most eukaryotic transcription factors (TFs) are part of large protein families, with members of the same family (i.e. paralogous TFs) recognizing similar DNA-binding motifs but performing different regulatory functions. Many TF paralogs are co-expressed in the cell, and thus can compete for target sites across the genome. Here, we show that direct competition for DNA binding between TF paralogs is a major determinant of their genomic binding patterns. more...

Organism:

synthetic construct; Saccharomyces cerevisiae

Type:

Other

Platform:

GPL29513

14 Samples

Download data: TXT

(Submitter supplied) The SELEX-seq platform was used to generate DNA-binding affinity predictions for the human Max transcription factor. This experiment was performed as part of a cross-validation study comparing the accuracy of DNA shape-augmented TF binding specificity models across two different platforms (SELEX-seq and gcPBM)

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

1 Sample

Download data: TXT

(Submitter supplied) Accurate predictions of the DNA binding specificities of transcription factors (TFs) are necessary for understanding gene regulatory mechanisms. Traditionally, predictive models are built based on nucleotide sequence features. Here, we employed three- dimensional DNA shape information obtained on a high-throughput basis to integrate intuitive DNA structural features into the modeling of TF binding specificities using support vector regression. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by array

Platform:

GPL17173

3 Samples

Download data: TXT

(Submitter supplied) Genomic analyses often involve scanning for potential transcription-factor (TF) binding sites using models of the sequence specificity of DNA binding proteins. Many approaches have been developed to model and learn a protein’s binding specificity by representing sequence motifs, including the gaps and dependencies between binding-site residues, but these methods have not been systematically compared. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL11260

172 Samples

Download data: TXT