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Dear Plinder Authors,
I have a quick question regarding the system files. I was reviewing the system `8q5i__1__1.GA__1.ZB`, but I noticed that the DNA complex seems to be missing from both the `sys…
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# ePlant3 Interactions View Blueprint and Requirements
by V. Lau (reviewed by N. Provart)
## Introduction
Genes and their gene products (proteins) can interact with other genes and gene produ…
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The web tool has support for new kinds of interactions we'd like to include eventually:
The output of Garnet should be changed to indicate what genes were used to predict a TF was important (i.e. t…
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Hi Nava,
I'm Roden Luo from the Gu Lab at University of Washington. We are developing a technology to detect protein-protein interactions via next generation DNA sequencing. I found your work, swif…
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Hello, the ENCODE project has another NTR request for an assay that we will need to annotate a number of experiments.
**editor preferred term:** Split-pool recognition of interactions by tag extens…
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* RNA-level predictions: free energy changes associated with nucleotide changes within a window (X bp before, X bp after) a nucleotide change; screen for RNAse targets within sequences (not sure if th…
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Hello @akundaje and @leepc12 ,
I wanted to use this pipeline to analyze ultra-low-input, native ChIP-Seq samples [ULI-NChIP](https://www.nature.com/articles/ncomms7033) looking at histone modifica…
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### [Transcription factors](https://www.youtube.com/watch?v=Sd3imcsvXxI)
1. Transcription factor (proteins) control the expression of genes by regulating the process of gene transcription.
![gene-…
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Hi
please could someone explain the difference between these two terms and then improve the definitions so that it is easier to choose which one to use:
GO:0140318 protein transporter activity
Mo…
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I suggest a reorganization of the categories to sort out current overlaps and redundancies and make icons easy to find.
After looking through the different categories I came up with the following b…