I see that RNA-seq assays have not been included. That's a shame. I was hoping to to try look at predicting expression from chromatin modifications. Oh well.
Not for the challenge, but I'm wondering if there are RNA-seq datasets available in a convenient format which I might try to do this with, i.e. I guess from the same samples as were used to generate the Challenge data?
Created by Dave Curtis DaveCurtis Great, thanks. No, I see now that this challenge is not about RNA-seq. I think when I saw the original description of the challenge I thought this would be included.
Thanks for those resources - I'll look into them.
Hi Dave,
I believe that is not the goal of this challenge...
however in ENCODE you have multiple expression data in multiple formats and multiple experiment types, like:
- shRNA RNA-seq
- polyA RNA-seq
- total RNA-seq
- small RNA-seq
- RNA microarray
- RAMPAGE
- microRNA-seq
- microRNA counts
- CAGE
- CRISPRi RNA-seq
- siRNA RNA-seq
- CRISPR RNA-seq
- polyA depleted RNA-seq
- RNA-PET
- single cell RNA-seq
Some references that might be interesting:
- Karli? et al. Histone modification levels are predictive for gene expression. doi.org/10.1073/pnas.0909344107
- Singh et al. DeepChrome: deep-learning for predicting gene expression from histone modifications. doi.org/10.1093/bioinformatics/btw427
- Wang et al. Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles. doi.org/10.1101/gr.201574.115
- Zhu et al. Modeling exon expression using histone modifications. doi.org/10.1371/journal.pone.0067448