GEO DataSets

(Submitter supplied) Transcription factor (TF) binding specificities (motifs) are essential to the analysis of noncoding DNA and gene regulation. Accurate prediction of TF sequence specificities is critical, because the hundreds of sequenced eukaryotic genomes encompass hundreds of thousands of TFs, and assaying each is currently infeasible. There is ongoing controversy regarding the efficacy of motif prediction methods, as well as the degree of motif diversification among related species. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL11260

682 Samples

Download data: TXT

(Submitter supplied) The nematode Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been hampered by the fact that DNA binding motifs are known for only 71 (9%) of the estimated 763 high-confidence sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray (PBM) experiments on representatives of canonical TF families in the C. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL11260

260 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

252 Samples

Download data: TXT

(Submitter supplied) C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2 arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. We have determined the binding sites and motifs of 119 C2H2 zinc finger proteins and the expression pattern of 80 cell lines overexpressing C2H2 zinc finger proteins in order to study the role of C2H2 zinc finger proteins in gene regulation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

92 Samples

Download data: TXT

(Submitter supplied) The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs), each of which typically binds a DNA nucleotide triplet within a larger binding site. Frequent recombination and diversification of their DNA-contacting residues suggests that these zinc fingers play a prevalent role in adaptive evolution. Very little is known about the function and evolution of the vast majority of C2H2-ZFs, including whether they even bind DNA. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

160 Samples

Download data: TXT

(Submitter supplied) Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. We present a computational method, dynamic motif occupancy (DynaMO), which exploits random forest modeling and clustering based enrichment analysis. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

30 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) Variations in noncoding regulatory sequences play a central role in evolution but interpreting such variations remains difficult even in the context of defined attributes such as transcription factor (TF) binding sites. Here, we systematically link variations in cis-regulatory sequences to TF binding by profiling the allele-specific binding of 27 TFs expressed in a yeast hybrid, which contains two related genomes within the same nucleus. more...

Organism:

Saccharomyces cerevisiae x Saccharomyces paradoxus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL31927 GPL22588

65 Samples

Download data: BEDGRAPH

(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) 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:

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:

GPL23293

4 Samples

Download data: TXT, XLSX

(Submitter supplied) Integration of whole-genome bisulfite sequencing with ChIPseq datasets.

Organism:

Mus musculus; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL21103 GPL20301

2 Samples

Download data: BEDGRAPH

(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