Evidence map›Paper›PMID 41959429›Full record

ArticlebioRxiv : the preprint server for biology2026

eSIG-Net: Accurate prediction of single-mutation induced perturbations on protein interactions using a language model.

Xingxin Pan, Aditya Shrawat, Sidharth Raghavan, Chuanpeng Dong, Yuntao Yang, Zhao Li, W Jim Zheng, S Gail Eckhardt, Erxi Wu, Juan I Fuxman Bass and 7 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. 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

17 authors.

Xingxin PanDepartment of Neurosurgery, Neuroscience Institute, Baylor Research Institute, Temple, TX 76508, USA.
Aditya ShrawatDepartment of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA.
Sidharth RaghavanDepartment of Neurosurgery, Neuroscience Institute, Baylor Research Institute, Temple, TX 76508, USA.
Chuanpeng DongDepartment of Genetics, and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
Yuntao YangMcWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030.
Zhao LiMcWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030.
W Jim ZhengMcWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030.
S Gail EckhardtDan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Erxi WuDepartment of Neurosurgery, Neuroscience Institute, Baylor Research Institute, Temple, TX 76508, USA.
Juan I Fuxman BassDepartment of Biology, Boston University, Boston, MA 02215, USA.
Daniel F JaroszDepartment of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Sidi ChenDepartment of Genetics, and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
Daniel J McGrailCenter for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195, USA.
Gloria M SheynkmanDepartment of Molecular Physiology and Biological Physics, Department of Biochemistry and Molecular Genetics, and UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
Jason H HuangDepartment of Neurosurgery, Neuroscience Institute, Baylor Research Institute, Temple, TX 76508, USA.
Nidhi SahniDepartment of Neurosurgery, Baylor College of Medicine, Temple, TX 76508, USA.
S Stephen YiDepartment of Neurosurgery, Neuroscience Institute, Baylor Research Institute, Temple, TX 76508, USA.ORCID 0000-0003-0047-8103

Funding

Tumor BiologyP30CA125123 · NCI · BAYLOR COLLEGE OF MEDICINE · PI Suzanne AW Fuqua · 2007 to 2026
$73.9M
Engagement and outreach to achieve a FAIR data ecosystem for the BICANU24MH130988 · NIMH · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI HUA XU, Guo-Qiang ZHANG · 2022 to 2026
$4.6M
Structure and Function of Immune Gene Regulatory NetworksR35GM128625 · NIGMS · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI Juan Ignacio Fuxman Bass · 2018 to 2026
$4.0M
Network-based Framework to Decode Novel Gain-of-Function Mutations and their Mechanistic Roles in General Human DiseasesR35GM133658 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI S. Stephen Yi · 2019 to 2026
$2.6M
Deciphering Functional Consequences of Specific and Combinatorial Mutations in Protein Interaction NetworksR35GM137836 · NIGMS · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI SAHNI, NIDHI · 2020 to 2023
$1.8M
Mechanisms of Action of Natural Genetic VariationR01HG012366 · NHGRI · STANFORD UNIVERSITY · PI Daniel Jarosz · 2023 to 2026
$1.5M
IMAT-ITCR Collaboration: A Cytoscape Toolkit to Model Proteoform-Resolved Cancer NetworksR33CA281919 · NCI · UNIVERSITY OF VIRGINIA · PI Gloria Sheynkman · 2024 to 2026
$1.3M
Determining the Immunological Consequences of DNA Replication Stress Response Defects in Renal Cells Carcinoma to Improve Immunotherapy OutcomesR00CA240689 · NCI · CLEVELAND CLINIC LERNER COM-CWRU · PI MCGRAIL, DANIEL JAMES · 2022 to 2024
$747k
NCI NIH HHS P30 CA125123NCI NIH HHS R00 CA240689NCI NIH HHS R33 CA281919NHGRI NIH HHS R01 HG012366NIGMS NIH HHS R35 GM128625NIGMS NIH HHS R35 GM133658NIGMS NIH HHS R35 GM137836NIMH NIH HHS U24 MH130988
6 · The paper itself

Abstract

Most proteins exert their functions in complex with other interactors. Single mutations can exhibit a profound impact on perturbing protein interactions, leading to human disease. However, predicting the effect of single mutations on protein interactions remains a major computational challenge. Deep learning, particularly protein language models or transformers, has become an effective tool in bioinformatics for protein structure prediction. However, the functional divergence of mutations makes it difficult to predict their interaction perturbation profiles. To address this fundamental challenge, we present

Identifiers

PMID41959429
PMCPMC13060096

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.