BondLab ENCODE Enabled Promoters (B.E.E.P.)
Welcome to the new BondLab ENCODE Enabled Promoter (BEEP) tool. It will take a list of gene names and names of transcription factors that have ENCODE ChIP-seq tracks, fetch the promoters of these genes, and map ENCODE ChIP-seq tracks to the set of promoters.
Click here for information on how to use B.E.E.P.
Resolves terms via QuickGO (same database as Gene Ontology). Human protein-coding symbols; counts should be close to the GOC browser (~800+ for inflammatory response).
Uses all 28,049 gene symbols in the hg38 RefSeq TSS cache (instant lookup; large BED download).
− = more 5′; + = toward 3′ (e.g. 0 = through TSS, +500 = 500 bp into gene)
Load the ENCODE Regulation TF Clusters track (hg38): ~340 TFs clustered from ENCODE ChIP-seq. Filtered to your step 1 promoter regions only (not the full 120 MB genome file).
Requires promoter BED from tab 1. First run may take 1–2 min on the server. Each site keeps its TF name from the cluster BED for overlap filtering.
Look up files directly from encodeproject.org by accession (e.g. from a track URL). Peak BED or bigWig both work; standard ChIP bigWig uses matching IDR peaks when available. Imputed ChromImpute bigWigs (e.g. ENCFF503NLL) have no peak BED — use bigWig signal overlap instead.
Note: with Add bigWig signal regions ticked, Build ChIP BED reads the bigWig. By default it scans only the genomic intervals covered by your step 1 promoter BED (merged per chromosome). Untick to scan all ~25 main chromosomes (slower, finds peaks outside your gene list). Leave the tab open until the status bar finishes.
Existing ChIP BED
After another ENCODE search: new search results are merged into the track list when adding; choose Replace to clear the previous ChIP set and start over.
Load ChIP intervals without ENCODE: paste or choose a BED, then click Load ChIP BED from paste/file or the main green button (no ENCODE tracks required). GRCh38 coordinates. Adds a new file unless you select one file in Files in ChIP set and use Append BED to selected file.
Files in ChIP set
Tracks and imports currently loaded. Select files to preview, append a BED into one file, or remove from the set.
Requires promoter BED (step 1) and ChIP BED (step 2). IDR peak BED omits many regions visible in the bigWig (e.g. chr1:247415462–247415583 in ENCFF397QRQ). Tick Add bigWig signal regions when building ChIP BED, or use bigWig signal overlap (finds signal islands in promoters with coordinates).
Multiple ChIP BED files in the set — tick which tracks to include in overlap, TF filter, and plots.
Build ChIP BED with multiple ENCODE tracks (e.g. NFYA and SREBP1), then filter promoters by which TFs
overlap. Leave blank for any overlap (default). Operators:
AND, OR, NOT, parentheses.
Examples: NFYA OR SREBP1 · NFYA AND SREBP1 ·
NFYA AND NOT SREBP1 · (NFYA OR SREBP1) AND NOT POLR2A
| Gene | RefSeq | Chr | Promoter (BED) | TF spacing | TFs | Peaks |
|---|
Promoter schematic
One row per overlapping gene (filtered). Pale bar = promoter; 5′ upstream on the left, TSS on the right (same layout for +/− strand). Tick marks = TF site centre; colors = TF. With max TF distance set, only sites from the passing proximity assignment are drawn (one site per TF in each AND group).
TF site frequency vs TSS
X = bp relative to TSS (0); negative = 5′ upstream, positive = into gene body. Each bin shows one bar per TF (colors match schematic and legend below). With max TF distance set, only sites from passing AND proximity groups are shown (same as schematic).
Different-TF pair frequency vs midpoint
Shown when Max TF peak distance is set. X = midpoint between pair centres (bp from TSS); only pairs with edge-to-edge distance ≤ max distance inside the promoter.