Transcription factors (TFs) control specificity and activity of gene transcription, but whether a relationship between these two features exists is unclear. Here we provide evidence for an evolutionary trade-off between the activity and specificity in human TFs encoded as submaximal dispersion of aromati...
To that end, we made the assumption that the true number of enriched regions between two compared conditions for a given mark or factor is similar and set the p parameter in the enrich mix function to 1. Finally, we obtained a list of candidates of differentially enriched regions at an ...
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Among them is the zinc-finger transcription factor, Yin and Yang (YY1), which has been shown to play a critical role in lung epithelial cell development and TGF-beta-induced lung fibrosis (Boucherat et al., 2015; Zhang et al., 2019). Another example is the expression of basic helix–...
Transcription factor. Target gene. Edge weight. zcat data-raw/regulatorycircuits/FANTOM5_individual_networks/394_individual_networks/synoviocyte.txt.gz|head RAX PPP2R2A 1.79016453E-3 MYCN RHOA 1.81311653E-2 TFAP2 RRM1 7.13096624E-3 PRDM4 KPNA2 1.61069158E-2 FOXB1 SCARF2 1.78696733E-3 ATF4 NDU...
We investigate whether introduction of new transcription factor binding sites due to HPV integration could invoke these changes. Some regions within the HPV genome, particularly the position of a conserved CTCF binding site, show enriched chromatin accessibility signal. ChIP-seq reveals that the ...
on our definition. The list of TF genes was derived from Ravasiet al.15, which is based on the manual curation of several sources: i) the TRANSFAC database; ii) genes annotated by the Gene Ontology (GO) term ‘transcription factor’; iii) genes that contain the word ‘transcription’ ...
To determine how well transcription can be predicted based on the de novo promoter sequences, we trained a CNN model (Methods) to predict the TSS positions genome-wide. To test the CNN, we first used it to score wild-type and mutant forms of the TERT promoter28,29(Methods); the model...
Octamer-binding transcription factor 4 PB-MNCs: Peripheral blood mononuclear cells PT-D: Post-transfection day qRT-PCR: Quantitative real-time RT-PCR RBC: Red blood cells SCF: Stem cell factor SSEA4: Stage-specific embryonic antigen 4 SOX2: Sex-determining region Y-box 2 VEGF: Va...
Table S1. List of Studies Profiling the Expression of SARS-CoV-2 Entry Factors in Human Tissues, Related to Figure 1 Table S2. List of SARS-CoV-2 and Coronavirus-Associated Receptors and Factors, or SCARFs, Related to Figure 1 Table S3. Overview of the Datasets Used in This Study, Rela...