The predictions are available on GRCh38/hg38 and T2T-CHM13/hs1. The contribution scores are available on GRCh38/hg38 only, because they are computed at MANE Select transcription start sites and MANE is not defined for T2T-CHM13.
Predictions are not measurements: they say what the sequence looks capable of, not what a given cell is doing. The matching experimental data is in the PRO-cap track, available on GRCh38/hg38.
-The matrix on this page has one row per cell line and one column per data type, -so a checkbox turns on one strand of one cell line's predictions, or its -contribution scores. Use the Sample class filter to restrict the matrix to -cancer or non-cancer lines. +This track collection holds one predicted PRO-cap track per cell line, shown by +default, and on GRCh38/hg38 one contribution score track per cell line, hidden by +default. Use the buttons on this page to turn tracks on or off, and click a track's +name to open its own settings, where the plus and minus strands of a predicted +PRO-cap track can also be turned on separately.
Each predicted PRO-cap track is an overlay of the two strands: plus strand predictions are drawn upward and minus strand predictions downward. The y axis is the predicted number of PRO-cap reads at that base.
Contribution scores are drawn as a sequence logo when zoomed in far enough to show individual bases: the letter of the reference base is scaled by its score, so a run of tall letters is a motif the model relied on. At lower zoom the same values are drawn as a wiggle. Scores can be negative, meaning the base argued against initiation being placed where it was. Scores exist only in the roughly 2 kb window around each MANE Select transcription start site, about 38.7 Mb of @@ -126,31 +127,32 @@ doc/$db/transcriptionStart.txt, the scripts they run are in makeDb/outside/proCapNet, and the track configuration is in trackDb/human/$db/transcriptionStart.ra.
The bigWig files are on our download server. Predictions are under pred/ and are named for the cell line, the model and the strand, for example K562.proCapNet.pos.bw and -K562.proCapNet.neg.bw. Contribution scores, which exist for GRCh38 only, +K562.proCapNet.neg.bw. Minus strand values are stored as negative +numbers. Contribution scores, which exist for GRCh38 only, are under contrib/, for example K562.proCapNet-contrib.bw.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-sep tables. From scripts, the data can be accessed through our API. The API returns one bigWig at a time, so name a single strand of one cell line rather than the container, for example track=proCapNet_K562_pred_pos.
Individual regions or the whole genome annotation can be obtained using our tool