BondLab ENCODE Enabled Promoters (B.E.E.P.)
B.E.E.P. builds BED files of human promoter coordinates from a local
GRCh38 RefSeq TSS cache (UCSC ncbiRefSeqCurated, same 10 bp TSS grouping
idea as Promoter Grabber), browses ENCODE transcription-factor ChIP-seq
tracks, converts peak calls to BED, and reports which promoters overlap factor binding.
WORKFLOW
-
Promoters — paste/upload gene symbols, pick a Gene Ontology term, or load
all ~28k cached human genes instantly. Set bases 5′ of TSS; download annotated BED
(
GENE_NM******) or standard BED3. -
ENCODE ChIP — search by TF/cell line, or paste file accessions
(
ENCFF368QGT.bigWig). Tick tracks; optional score threshold; separate or merged BED. -
Overlap — promoters overlapping ChIP peaks → gene table; annotated BED
(
GENE_NM_*_AND_TP53) or standard BED3 (coordinates only).
Promoter coordinates: cached UCSC RefSeq (GRCh38/hg38). GO gene lists: QuickGO. ENCODE: REST API.
Coordinates only (no sequence). BED column 4 = GeneSymbol_NM accession. Strand in column 6.
Lookups use bundled hg38 RefSeq TSS cache (~28k genes; max 5000 per custom list).
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)
Browse ENCODE TF ChIP-seq (GRCh38). Peak BED is preferred; bigWig selections use the matching IDR peak file from the same dataset when available.
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.
After building ChIP BED, append regions from a downloaded or external BED (GRCh38). Does not replace ENCODE peaks — rows are added to the current 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).
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 |
|---|