Evidence map›Paper›PMID 38853896›Full record

ArticlebioRxiv : the preprint server for biology2024

Dissecting the

Kelly Cochran, Melody Yin, Anika Mantripragada, Jacob Schreiber, Georgi K Marinov, Sagar R Shah, Haiyuan Yu, John T Lis, Anshul Kundaje

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Kelly CochranDepartment of Computer Science, Stanford University, Stanford, CA, USA.ORCID 0000-0001-5481-2344
Melody YinThe Harker School, San Jose, CA, USA.
Anika MantripragadaThe Harker School, San Jose, CA, USA.
Jacob SchreiberDepartment of Genetics, Stanford University, Stanford, CA, USA.
Georgi K MarinovDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0003-1822-7273
Sagar R ShahDepartment of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
Haiyuan YuDepartment of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.ORCID 0000-0001-7597-6049
John T LisDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.ORCID 0000-0003-1201-9406
Anshul KundajeDepartment of Computer Science, Stanford University, Stanford, CA, USA.ORCID 0000-0003-3084-2287

Funding

GENCODE: comprehensive reference genome annotation for human and mouseU24HG007234 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Fergal James Martin · 2021 to 2026
$16.1M
Predicting context-specific molecular and phenotypic effects of genetic variation through the lens of the cis-regulatory codeU01HG012069 · NHGRI · STANFORD UNIVERSITY · PI Anshul Kundaje · 2021 to 2026
$3.9M
Decoding the regulatory architecture of the human genome across cell types, individuals and diseaseU01HG009431 · NHGRI · STANFORD UNIVERSITY · PI PRITCHARD, JONATHAN K · 2017 to 2021
$3.5M
NHGRI NIH HHS U01 HG009431NHGRI NIH HHS U01 HG012069NHGRI NIH HHS U24 HG007234
6 · The paper itself

Abstract

Despite extensive characterization of mammalian Pol II transcription, the DNA sequence determinants of transcription initiation at a third of human promoters and most enhancers remain poorly understood. We trained and interpreted a neural network called ProCapNet that accurately models base-resolution initiation profiles from PRO-cap experiments using local DNA sequence. ProCapNet learns sequence motifs with distinct effects on initiation rates and TSS positioning and uncovers context-specific cryptic initiator elements intertwined within other TF motifs. ProCapNet annotates predictive motifs in nearly all actively transcribed regulatory elements across multiple cell-lines, revealing a shared

Identifiers

PMID38853896
PMCPMC11160661

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.