7
votes
How do you query and explore ENCODE data?
I don't know whether there is an API, but ENCODE's website does provide an interactive data matrix where you can filter data based on assay and sample type, place data sets in a "shopping cart", and ...
- 5,110
6
votes
Accepted
Biohackers Netflix - DNA to binary and video
I was quite curious when I saw that as well. I've spent more time than I'd care to admit trying the sort of things you have. I've gotten it decoded now, but I can't really claim any sort of victory, ...
- 176
6
votes
Accepted
What is the difference between ENCODE Tier 1, 2 and 3 cell types?
The tiers denote the original priority of sequencing and processing the samples. This is understandable given the number of marks and experiment types that ENCODE tried to sequence. Further details ...
- 19.8k
5
votes
How do you query and explore ENCODE data?
You can just add /?format=json to any page to get the JSON output.
ENCODE REST API documentation: https://www.encodeproject.org/help/rest-api/
Example scripts: ...
- 2,209
5
votes
Given a transcription factor, what genes does it regulate?
MSigDB has a collection (C3:TFT) of gene sets corresponding to transcription factor targets.
Harmonizome has functional terms for genes extracted from over a hundred publicly available resources.
- 2,209
4
votes
Given a transcription factor, what genes does it regulate?
In general, there is two options to identify targets for transcription factors: experimental (ChIP-seq) and sequence-based predictions.
TF binding from experimental data
The are multiple projects ...
- 300
4
votes
Given a transcription factor, what genes does it regulate?
iRegulon takes a sequence-based approach to finding transcription factor targets. There's a Cytoscape app that you can use to find the regulators of a given gene list, or the targets of a particular ...
- 861
2
votes
Accepted
Transcription factor targets for Human and Mouse genes
JASPAR is another useful transcription factor profiling database.
The JASPAR CORE contains a curated, non-redundant set of profiles, derived from published and experimentally defined transcription ...
- 66
2
votes
How do you query and explore ENCODE data?
So let's say I want to get the bed file of this experiment using curl encodeproject.org/experiments/ENCSR000CKC
You can also search for files that belong to a ...
- 21
1
vote
Transcription factor targets for Human and Mouse genes
JASPAR is only based on TF motifs, which are very short sequences and not enough to precisely tell you the true TF-motif relationships, especially when multiple TFs have complex logic gates regulating ...
- 292
1
vote
How to visualize genome track of gene in specific cell-lines?
Like others have mentioned, these plots come from BAM, BED, and BigWig files.
Those files contain the data that you can give to tools like the UCSC Genome Browser, IGV, HiGlass/Gosling, or other ...
- 1,394
1
vote
How to visualize genome track of gene in specific cell-lines?
Answer from @devon-ryan, converted from comments:
You'll need BAM or bigWig files for each of the tracks. If you can't find any you'll have to make them yourself from public fastq files. The fastq ...
1
vote
How to visualize genome track of gene in specific cell-lines?
You can use screen.encodeproject.org
It collected a lot of data from multiple cell lines or tissues. And you can export tracks to UCSC browser or other browsers.
- 292
1
vote
What is the difference between ENCODE Tier 1, 2 and 3 cell types?
From Encode's website:
... To aid in the integration and
comparison of data produced using different technologies and
platforms, the ENCODE Consortium has designated cell types that will
be ...
- 111
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