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 2.1k

System / cell line: expression ✕ Clear

Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

PMID 32714363 · PMC7344232 · Frontiers in genetics · 2020 · 6 claims · 6 setups

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The midnight blue module and the yellow module play vital roles in the pathogenesis of CAD in non-diabetic patients

pbmcs blood apoe genes microarray rt-qpcr elisa
Solute exchange through gap junctions lessens the adverse effects of inactivating mutations in metabolite-handling genes.

PMID 36107487 · PMC9534548 · eLife · 2022 · 8 claims · 8 setups

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Colorectal cancer (CRC) cells are coupled by gap junctions assembled predominantly from Cx26 (GJB2)

colorectal normal crc microarray tcga single-cell
Exploration of effective biomarkers for venous thrombosis embolism in Behçet's disease based on comprehensive bioinformatics analysis.

PMID 38987624 · PMC11236978 · Scientific reports · 2024 · 6 claims · 8 setups

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Four hub genes (E2F1, GATA3, HDAC5, MSH2) serve as diagnostic biomarkers for VTE in BD with high accuracy (AUC 0.816)

peripheral degs candidate microarray weighted protein–protein
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

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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
Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.

PMID 39775580 · PMC11684664 · PloS one · 2024 · 7 claims · 8 setups

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MitoDEGs in MI are mainly involved in mitochondrial function and ATP synthesis pathways

left mus combined heart microarray weighted bulk
PPDPF is not a key regulator of human pancreas development.

PMID 40193385 · PMC12037078 · PLoS genetics · 2025 · 8 claims · 8 setups

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PPDPF is not a key regulator of human pancreas development, in contrast to its zebrafish orthologue exdpf

fetuses fetal hesc population situ proteome qpcr
Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

PMID 40857330 · PMC12380325 · PloS one · 2025 · 6 claims · 8 setups

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90 interacting genes were identified at the intersection of AAA DEGs and periodontitis WGCNA module genes

abdominal gingival overlapping interacting microarray weighted kegg
Identification of a pediatric acute hypoxemic respiratory failure signature in peripheral blood leukocytes at 24 hours post-ICU admission with machine learning.

PMID 37009294 · PMC10063855 · Frontiers in pediatrics · 2023 · 7 claims · 5 setups

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A machine learning stability selection approach (bootstrapped logistic regression, 100 simulations) can identify genes associated with PaO2/FiO2 < 200 vs ≥200 when standard differential expression with FDR correction shows no overlap between cohorts.

pediatric combined top-ranked whole-blood machine pathway
Integrative microRNA and transcriptome analysis reveals sex-specific molecular divergence in human bladder cancer.

PMID 41578372 · PMC12911049 · Biology of sex differences · 2026 · 8 claims · 8 setups

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48 tumor-specific sex-biased (TSSB) microRNAs were identified in bladder cancer, mostly located on autosomes rather than sex chromosomes

tcga tssb blca mirna-seq bulk kegg
Major transitions in early coral development: novel insights enabled by visualisation of a comprehensive transcriptomic dataset for Acropora millepora.

PMID 41612263 · PMC12924552 · BMC biology · 2026 · 8 claims · 6 setups

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Profiling gene expression across 26 life stages of A. millepora and building an interactive Shiny-based tool (DEView) enables comprehensive visualisation of developmental transcriptomic data.

acropora millepora bulk differential pca
A cost-effective and scalable barcoded library construction method for deep mutational scanning studies.

PMID 41671286 · PMC12923136 · PLoS biology · 2026 · 8 claims · 4 setups

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A two-step cloning strategy (Gibson assembly followed by Golden Gate assembly) using degenerate oligo pools (oPools) with co-synthesized DNA barcodes enables construction of scalable DMS libraries for large genes.

yeast short-read transformation barcode
Protocol to perform cell-type-specific transcriptome-wide association study using scPrediXcan framework.

PMID 41689808 · PMC12925207 · STAR protocols · 2026 · 6 claims · 6 setups

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scPrediXcan enables cell-type-specific transcriptome-wide association studies (TWAS) by integrating deep learning-based prediction of gene expression from DNA sequence and epigenetic features.

acinar individual-level geuvadis beta mlp-based personalized elastic-net
BCR::ABL1-Induced Enhancer Reprogramming Uncovers Hypersensitivity of Ph+B-ALL Cells to Enhancer-Targeting Drugs.

PMID 41764406 · PMC13137836 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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BCR::ABL1-induced malignant transformation and transcriptional reprogramming of B-cell precursors is accompanied by genome-wide enhancer (non-promoter H3K27ac) activation

b-cell ph+b-all tom-1 lines rna-seq promoter-capture western
Resource Availability Modulates Gene Expression Across Life Stages in a Migratory Butterfly.

PMID 41797265 · PMC12968515 · Molecular ecology · 2026 · 7 claims · 6 setups

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Adult female exposure to host plants for egg-laying is associated with differential expression of ecdysteroid and juvenile-hormone pathway genes, consistent with endocrine regulation of reproductive readiness and the oogenesis–flight syndrome

vanessa bulk gene kegg
PeakPrime: a peak-guided primer design pipeline for target enrichment in 3'-end RNA-seq.

PMID 41919010 · PMC13034549 · Bioinformatics advances · 2026 · 8 claims · 7 setups

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PeakPrime is a reproducible Nextflow pipeline that calls 3′ RNA-seq coverage peaks (MACS2), selects exonic windows, designs strand-appropriate primers (Primer3), and screens specificity (Bowtie2)

imr-32 universal candidate 10m-read rna-seq targeted quantitative
MiR-21-5p Protects Embryonic Growth and Heart Function During Developmental Hypoxia by Dampening HIF Responses and Altering Gene Expression.

PMID 42138560 · PMC13178401 · Comprehensive Physiology · 2026 · 8 claims · 7 setups

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Hypoxia induces widespread transcriptomic remodeling in neonatal rat cardiomyocytes (385 DEGs vs normoxia)

neonatal chicken fetal tunel long-read exon-level
Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution.

PMID 41388990 · PMC12776951 · The Plant cell · 2026 · 8 claims · 6 setups

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MERFISH was successfully optimized for wheat inflorescence tissue, enabling localization of a 200-gene panel to cellular resolution across 4 developmental stages

microdissected cryosectioned wheat merfish-imaged bulk merfish single-nucleus
Comparative Transcriptomic Profiling Identifies IL-1β as a Non-Canonical Driver of Human Dendritic Cell Maturation.

PMID 41472934 · PMC12745711 · Iranian journal of biotechnology · 2026 · 8 claims · 7 setups

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IL-1β can substitute for PAMPs in inducing DC maturation via a non-canonical pathway distinct from classical TLR-mediated activation

monocyte-derived dendritic bulk principal pathway
Annexin A13 Protects Against Acute Kidney Injury by Inactivating TGF-β/Smad3 Signaling.

PMID 41486854 · PMC12915081 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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ANXA13 is selectively downregulated in the kidneys of AKI patients and IRI- or cisplatin-induced AKI mice, primarily in proximal tubular cells

kidney aki renal hek293t rna-seq immunohistochemistry serum
Unraveling the Causal Linkages of RBP7 and SCGB3A1 on Pelvic Organ Prolapse: Multifaceted Insights From Genome-Wide Mendelian Randomization, Single-Cell RNA Analysis, and Network Pharmacology.

PMID 41497737 · PMC12765987 · BioMed research international · 2026 · 8 claims · 7 setups

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High RBP7 expression causally increases POP risk

vaginal gwas rbp7 key single-cell mendelian protein-protein

Experiments

Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

Solute exchange through gap junctions lessens the adverse effects of inactivating mutations in metabolite-handling genes.

Exploration of effective biomarkers for venous thrombosis embolism in Behçet's disease based on comprehensive bioinformatics analysis.

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

Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.

PPDPF is not a key regulator of human pancreas development.

Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

Identification of a pediatric acute hypoxemic respiratory failure signature in peripheral blood leukocytes at 24 hours post-ICU admission with machine learning.

Integrative microRNA and transcriptome analysis reveals sex-specific molecular divergence in human bladder cancer.

Major transitions in early coral development: novel insights enabled by visualisation of a comprehensive transcriptomic dataset for Acropora millepora.

A cost-effective and scalable barcoded library construction method for deep mutational scanning studies.

Protocol to perform cell-type-specific transcriptome-wide association study using scPrediXcan framework.

BCR::ABL1-Induced Enhancer Reprogramming Uncovers Hypersensitivity of Ph+B-ALL Cells to Enhancer-Targeting Drugs.

Resource Availability Modulates Gene Expression Across Life Stages in a Migratory Butterfly.

PeakPrime: a peak-guided primer design pipeline for target enrichment in 3'-end RNA-seq.

MiR-21-5p Protects Embryonic Growth and Heart Function During Developmental Hypoxia by Dampening HIF Responses and Altering Gene Expression.

Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution.

Comparative Transcriptomic Profiling Identifies IL-1β as a Non-Canonical Driver of Human Dendritic Cell Maturation.

Annexin A13 Protects Against Acute Kidney Injury by Inactivating TGF-β/Smad3 Signaling.

Unraveling the Causal Linkages of RBP7 and SCGB3A1 on Pelvic Organ Prolapse: Multifaceted Insights From Genome-Wide Mendelian Randomization, Single-Cell RNA Analysis, and Network Pharmacology.