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Hi @mariam16548
Today let's create a full-chromosome or maybe even whole genome study of a transcription factor (TF) with more length (and thus more binding complexity) that GATA1. We might exp…
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- EXP annotations to this term are here:
https://docs.google.com/spreadsheets/d/17UgKKsxtQveZW9o5cvqlaNpGS5Zx2ymZVkdW9vZjzxc/edit#gid=0
(Edited to make clearer):
GO:0006351 transcription, DNA-…
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https://doi.org/10.1101/170761
> How to extract informative features from genome sequence is a challenging issue. Gapped k-mers frequency vectors (gkm-fv) has been presented as a new type of featur…
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Identify at least 2, ideally 3 alternative methods that can use prior information (known targets of transcription factors) to predict TF activities on single-cell transcriptomic profiles.
These met…
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From the 2023-10-12 Reactome2GO meeting at NYU:
In the [nuclear signaling by ERBB4 model](https://reactome.org/PathwayBrowser/#/R-HSA-1236394&SEL=R-HSA-1251985&PATH=R-HSA-162582,R-HSA-9006934), the…
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`Activity` could represent a particular Molecular function that participates or that is targeted in the causal statement. This information seems to be important when highlighting causality between ent…
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I think we've discussed this in the past, but I didn't see an issue commemorating it. The basic idea is that there are things like repeats (or other features that may be of interest in some specialize…
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https://doi.org/10.1109/BIBM.2016.7822515 (https://arxiv.org/abs/1611.05777)
> Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promot…
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```Without cell-specific features, another solution could be to use domain adaptation methods where the model trains on a source cell type and uses unsupervised feature extraction methods to predict o…
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There are quite a few annotations to DNA replication and nucleocytoplasmic transport. Most of these are derived from the THO complex which is involved in transcription and export. If you mutate the TH…