Clustering of Direct and Indirect DNA Binding Motifs of Human and Mouse Transcription Factors: X-TFBS Compendium from ChIP-seq
Sharov, A. A.
Show abstract
Uncovering networks of gene expression regulation requires knowledge of specific DNA-binding motifs of transcription factors (TFs). Most TFs have multiple DNA motifs enriched in its ChIP-seq peak regions because of protein interaction and spatial correlation between TFs and cofactors. To capture both direct binding and indirect association of TFs with specific DNA locations, all-against-all relations are identified here between TFs and DNA-binding motifs by the reanalysis of 8027 human and 2820 mouse ChIP-seq experiments from GEO. DNA motifs were analyzed with CisFinder and then clustered using the new k-mean algorithm tailored for this kind of data. Additional clusters of motifs were found by filtering ChIP-seq peaks based on their location in promoters, enhancers, and repeat-depleted regions. The new X-TFBS compendium, which includes 1157 human and 536 mouse clusters bound by 459 orthologous human-mouse pairs of TFs, 1038 human-only, and 165 mouse-only TFs, is the largest among existing databases. Most orthologous TFs in human and mouse have nearly identical DNA-binding motifs. Clustering helps to annotate TF-binding motifs and evaluate interactions between TFs that are associated with the same motif. Visual comparison of large sets of DNA motifs is simplified by using sequence script instead of sequence logo.
Matching journals
The top 13 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Dynamical gene regulatory networks are tuned by transcriptionalautoregulation with microRNA feedback. 95%
- Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions 95%
- L1PA2 transposons contribute abundant regulatory sequences in MCF7 breast cancer cell line 94%
Similar papers in this journal
- A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome 93%
- Harnessing changes in open chromatin determined by ATAC-seq to generate insulin-responsive reporter constructs. 91%
- Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response 91%
Similar papers in this journal
- Evolutionary Perspective And Expression Analysis Of Intronless Genes Highlight The Conservation On Their Regulatory Role 94%
- Characterization of Human Dosage-Sensitive Transcription Factor Genes 93%
- Integrative Ranking Of Enhancer Networks Facilitates The Discovery Of Epigenetic Markers In Cancer 93%
Similar papers in this journal
- ANANSE: An enhancer network-based computational approach for predicting key transcription factors in cell fate determination 94%
- To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq 94%
- CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length 94%
Similar papers in this journal
- Rapid gene evolution in an ancient post-transcriptional and translationalregulatory system compensates for meiotic X chromosomal inactivation 93%
- Ascertainment bias in the genomic test of positive selection on regulatory sequences 92%
- Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements 91%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.