MapRRCon Analysis of ENCODE ChIP-seq Datasets on LINE-1


MapRRCon database contains Transcription Factor (TF) enrichment profiles on various families of LINE-1 retrotransposons.

This website is designed to visualize coverage, peaks and motifs of specific TFs on L1. We also provide TF binding profile comparisons of multiple L1 families on a subset of hESC datasets.

(more cell lines will be available soon)


To start your search, please enter a name of transcription factor in the search box.

For more detailed instructions please click the help button located in the top right corner of the page.

In the MapRRCon pipeline, ChIP-seq data are first aligned to the human reference sequence hg38. Both unique (filled gray boxes) and multiply aligned reads (hollow gray boxes) are then extracted and mapped to the 1620 annotated L1HS sites based on their genome coordinates. We exclude reads with partial alignment (soft clipping), more than 3 mismatches and any indels (boxes with red lines). Filtered reads are subsequently mapped to L1HS consensus sequence to obtain compiled reads. Finally, we generate coverage profiles for both ChIP and INPUT data and then perform median-based normalization. We then call peaks from the normalized data using a self-developed algorithm that is specifically designed for short consensus sequences.

All the ChIP-seq data is available from the ENCODE website.

The methodology and analyzed data is described in the following paper:

Xiaoji Sun, Xuya Wang, Zuojian Tang, Mark Grivainis, David Kahler, Chi Yun, Paolo Mita, David Fenyƶ, Jef D. Boeke. Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression. Proc Natl Acad Sci U S A. 2018 May 25. pii: 201722565. doi: 10.1073/pnas.1722565115.

Click here to download the scripts used by MapRRCon