Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 23

System / cell line: in-silico ✕ Assay: gsea ✕ Clear

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

PMID 32898168 · PMC7478592 · PLoS biology · 2020 · 8 claims · 8 setups

Has reproduction · 89

SARS-CoV-2 infection induces a strong interferon-driven antiviral response in the nasopharynx, with up-regulation of viral sensors, T cell/NK chemokines, and antiviral effectors

nasopharyngeal airway patient-matched swab shotgun gsea biological
Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension.

PMID 36277786 · PMC9582241 · Frontiers in cardiovascular medicine · 2022 · 7 claims · 8 setups

Has reproduction · 73

FBXW4 and 13 other genes are uniquely enriched in the general hypertension group

peripheral white four gse75360 microarray gene weighted
Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

Has reproduction · 64

Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

heart degs dgat2 mitodegs microarray kegg protein-protein
Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.

PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups

Has reproduction · 66

At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls

subcutaneous sat rhesus bulk gsea xcell
Network Controllability Reveals Key Mitigation Points for Tumor-Promoting Signaling in Tumor-Educated Platelets.

PMID 41226816 · PMC12609506 · International journal of molecular sciences · 2025 · 8 claims · 6 setups

Has reproduction · 84

TEPs from NSCLC patients show 111 upregulated and 108 downregulated genes compared to platelets from non-cancer donors

platelets degs platelet-specific tep-specific transcriptome pathway k-means
Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

PMID 39074091 · PMC11285958 · PloS one · 2024 · 7 claims · 8 setups

Full-text index only

JAG, DLL, and NOTCH family gene/protein expression varies diversely across 15 cancer types relative to normal tissue, sometimes discordant between mRNA and protein levels.

tumor degs cancer jag bulk proteomics gene
Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.

PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 8 setups

Has reproduction · 75

The three mouse models (5xFAD, APP/PS1, hAβ-KI) share more DEGs and GOBP terms with LOAD than with EOAD patients

hippocampus postmortem computational bulk publicly qrt-pcr
Enterotoxins A and B produced by Staphylococcus aureus increase cell proliferation, invasion and cytarabine resistance in acute myeloid leukemia cell lines.

PMID 37810000 · PMC10559070 · Heliyon · 2023 · 8 claims · 8 setups

Has reproduction · 88

SEA and SEB treatment increases cell proliferation in AML cell lines

aml cgp differentially proliferation culture transwell
Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.

PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups

Has reproduction · 59

Short-term stress and long-term adaptations share common metabolic pathways

great embryonic gef mapk1 bulk gene transcription
TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila.

PMID 40314147 · PMC12774851 · Genetics · 2026 · 8 claims · 8 setups

Full-text index only

TF2TG is an online resource integrating motif scan data, ChIP-seq peaks (modENCODE/modERN), Hi-C (TADs), REDfly-curated CRMs, ATAC-seq, protein-protein interaction data, and tissue-specific expression to predict TF-target gene relationships in Drosophila

drosophila combined motif chip-seq whole-animal
pmid-42074497

PMID 42074497 · PMC13116960 · 8 claims · 6 setups

Full-text index only

Ionizing radiation induces extensive transcriptome reprogramming in mouse bone marrow HSCs 3 days after whole-body irradiation.

bone deg transcriptome deg-encoded rna-seq gene kegg
Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

Full-text index only

Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

luad demtdmrgs gse131907 wgcna kegg univariate
Splicing variants in MYRF cause partial loss of function in the retinal pigment epithelium leading to nanophthalmos.

PMID 41746734 · PMC13043084 · JCI insight · 2026 · 8 claims · 8 setups

Full-text index only

The dG-MYRF C-terminal frameshift variant undergoes normal homotrimerization, cleavage, and nuclear localization but shows reduced steady-state levels of the C-terminal cleavage product and decreased transcriptional activation of target genes.

arpe-19 myrf rpe e17.5 immunofluorescence computational cycloheximide
Targeting KIFC1 to disrupt centrosome clustering and trigger anaphase catastrophe in small-cell lung cancer.

PMID 41948931 · PMC13134724 · JCI insight · 2026 · 8 claims · 8 setups

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KIFC1 is overexpressed in SCLC compared with normal tissues and other cancer types

sclc h146 clinical cancer immunofluorescence viability flow
Distinct tumor genomic signatures underlie canine macrophage polarization.

PMID 42030266 · PMC13108725 · PloS one · 2026 · 8 claims · 8 setups

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Canine cancer cell lines show marked heterogeneity in macrophage polarization capacity, largely independent of histologic tumor type

monocyte-derived canine dh82 rna-seq elisa 13-plex bulk
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups

Has reproduction · 71

AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

aml hovon cancer tcga bulk consensus machine
Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.

PMID 35509605 · PMC9058021 · International journal of general medicine · 2022 · 8 claims · 8 setups

Has reproduction · 59

NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering

tcga-nsclc geo bulk microarray unsupervised
Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss.

PMID 41719400 · PMC12922754 · Science advances · 2026 · 8 claims · 8 setups

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Subclustering of ccRCC tumor cells reveals four shared epigenetic programs (C0-C3) recurrent across patients, cohorts, and disease stages

rcc internal tumor state-specific single-cell multiome copy
Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

PMID 38230570 · PMC10795782 · Cancer biology & therapy · 2024 · 8 claims · 6 setups

Has reproduction · 87

NOR-specific and MES-specific gene expression patterns are largely mutually exclusive, exhibiting a teams-like behavior across multiple bulk NB transcriptomic datasets

lines bulk single-cell housekeeping bulk pca single-sample
Epigenetic profiling of hematopoietic stem cells from male mice identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response.

PMID 41720793 · PMC13035812 · Nature communications · 2026 · 8 claims · 8 setups

Full-text index only

Lifelong CR reduces white blood cell production and shifts hematopoiesis toward myeloid and thrombo-erythroid lineages while suppressing lymphoid output

peripheral sorted young aged complete flow bulk

Experiments

Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila.

pmid-42074497

Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

Splicing variants in MYRF cause partial loss of function in the retinal pigment epithelium leading to nanophthalmos.

Targeting KIFC1 to disrupt centrosome clustering and trigger anaphase catastrophe in small-cell lung cancer.

Distinct tumor genomic signatures underlie canine macrophage polarization.

Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss.

Epigenetic profiling of hematopoietic stem cells from male mice identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response.