Questions tagged [encode]

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1answer
72 views

Transcription factor targets for Human and Mouse genes

I want to get transcription factor targets for my list of genes (For Human and Mouse) I have found ENCODE Transcription Factor Targets database (The link is given below). But I am looking for some ...
5
votes
3answers
147 views

How do you query and explore ENCODE data?

I am looking for a modular way to query data from ENCODE. For example, I would like to get CHiP-seq or similar tracks for a specific cell line. What's the proper way to do it? Finally, is there an ...
3
votes
0answers
63 views

Details of ENCODE processing pipelines

I am trying to find details for how the ENCODE ChIP seq samples were processed. Linking to a ChIPseq samples on www.encodeproject.org (e.g. https://www.encodeproject.org/experiments/ENCSR051DXE/) ...
2
votes
0answers
50 views

How to visualize genome track of gene in specific cell-lines?

I'm trying to make a plot showing genome tracks of specific genes in specific cell-lines of RNA-seq and Chip-seq data. It should look something like this I have recently seen this encode, but in ...
7
votes
4answers
179 views

Given a transcription factor, what genes does it regulate?

I have a list of transcription factors and I am interested in finding out which which genes might be transcribed as a result of the formation of transcription factor complexes with that transcription ...
7
votes
2answers
312 views

What is the difference between ENCODE Tier 1, 2 and 3 cell types?

The ENCODE Experiment Matrix at UCSC lists the different available cell types under the categories "Tier 1", "Tier 2" and "Tier 3". What is the difference between these classifications? What, for ...