Evidence map›Paper›PMID 39605368›Full record

ArticlebioRxiv : the preprint server for biology2024

GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors.

Arttu Jolma, Aldo Hernandez-Corchado, Ally W H Yang, Ali Fathi, Kaitlin U Laverty, Alexander Brechalov, Rozita Razavi, Mihai Albu, Hong Zheng, Codebook Consortium and 3 more

Abstract readPreprint
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

5 · Who and what money

Authors and funding

13 authors.

Arttu JolmaDonnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.ORCID 0000-0002-2543-7490
Aldo Hernandez-CorchadoDepartment of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada.ORCID 0000-0003-0682-3959
Ally W H YangDonnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.ORCID 0000-0002-8678-0946
Ali FathiDepartment of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.ORCID 0009-0007-1441-9653
Kaitlin U LavertyDonnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.ORCID 0009-0004-4341-4665
Alexander BrechalovDonnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
Rozita RazaviDonnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.ORCID 0009-0000-5466-6519
Mihai AlbuDonnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
Hong ZhengDonnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
Codebook Consortium
Ivan V KulakovskiyVavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia and Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Russia.
Hamed S NajafabadiDepartment of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada.
Timothy R HughesDonnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4M
Tissue Repository CoreP30AR070549 · NIAMS · CINCINNATI CHILDRENS HOSP MED CTR · PI Leah Claire Kottyan · 2016 to 2026
$7.7M
Gene regulatory network modeling of disease-associated DNA methylation perturbationsR01AI173314 · NIAID · CINCINNATI CHILDRENS HOSP MED CTR · PI Minji Byun, Emily Miraldi · 2023 to 2026
$3.1M
Post-transcriptional Regulatory NetworksR01HG013328 · NHGRI · SLOAN-KETTERING INST CAN RESEARCH · PI Quaid Morris · 2023 to 2026
$2.6M
Transcription Factor Genetics in LupusR01AR073228 · NIAMS · CINCINNATI CHILDRENS HOSP MED CTR · PI KOTTYAN, LEAH CLAIRE, WAGGONER, STEPHEN N. · 2019 to 2023
$2.2M
CisBP and CisBP-RNA: web resources for protein-DNA and protein-RNA binding modelsU24HG013078 · NHGRI · CINCINNATI CHILDRENS HOSP MED CTR · PI Matthew Tyson Weirauch · 2024 to 2026
$1.6M
Measuring and describing nucleosome remodeler sequence preferencesR21HG012258 · NHGRI · UNIVERSITY OF TORONTO · PI HUGHES, TIMOTHY · 2022 to 2022
$267k
NCI NIH HHS P30 CA008748NHGRI NIH HHS R01 HG013328NHGRI NIH HHS R21 HG012258NHGRI NIH HHS U24 HG013078NIAID NIH HHS R01 AI173314NIAMS NIH HHS P30 AR070549NIAMS NIH HHS R01 AR073228
6 · The paper itself

Abstract

A long-standing challenge in human regulatory genomics is that transcription factor (TF) DNA-binding motifs are short and degenerate, while the genome is large. Motif scans therefore produce many false-positive binding site predictions. By surveying 179 TFs across 25 families using >1,500 cyclic

Indexed as

C2H2C2H2 zinc fingerChIP-SeqCodebookDNA binding specificityGene regulationGHT-SELEXHT-SELEXMAGIXModular bindingPosition weight matrixPWMRCADEEMSELEXTFTranscription factorTranscription factor binding site

Identifiers

PMID39605368
PMCPMC11601218

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.