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).

• Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.

  PMID 33890574 · PMC8104967 · eLife · 2021 · 8 claims · 8 setups

  Has reproduction · 76

  FOXM1 and RHNO1 are head-to-head bidirectional genes regulated by a shared bidirectional promoter (F/R-BDP)

  tcga ft282 gistic expression rt-qpcr

• 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

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

  luad demtdmrgs gse131907 wgcna kegg univariate

• Integrating co-expression network analysis and machine learning to reveal the regulatory landscape of GPD genes in Chlamydomonas reinhardtii under salinity stress.

  PMID 42004709 · PMC13089224 · PeerJ · 2026 · 8 claims · 8 setups

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  GPD2 and GPD3 cluster into distinct WGCNA co-expression modules (magenta and black, respectively) with contrasting temporal expression profiles

  chlamydomonas genes normalized gpd bulk weighted gene

• A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

  PMID 28642491 · PMC5481429 · Scientific reports · 2017 · 8 claims · 8 setups

  Has reproduction · 76

  Hnf4a is a major transcriptional regulator of Dnajc22

  atlas roadmap liver-specific kidney co-expression transcription reanalysis

• 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

• PVT1 lincRNA signals an androgen-dependent transcriptional activation program of oncogenes in prostate cancer cells.

  PMID 41792045 · PMC13139993 · International journal of cancer · 2026 · 8 claims · 7 setups

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  PVT1 knockdown significantly reduces LNCaP cell proliferation and increases sensitivity to apoptosis

  lncap tcga-prad rt-qpcr trypan transwell

• Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.

  PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 80

  WGCNA identified 214 key genes in the blue module most correlated with LUAD

  tcga-luad merged tedc2-associated a549 wgcna differential machine

• Dopamine enhances surface glial glycolysis via acetylcholine and insulin/insulin-like growth factor signaling in the honeybee.

  PMID 41797926 · PMC12964235 · iScience · 2026 · 8 claims · 5 setups

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  Bromocriptine (dopamine receptor agonist) increases glycolytic flux in forager bee brains

  forager targeted qpcr single-cell

• Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

  PMID 34643182 · PMC8555986 · eLife · 2021 · 7 claims · 8 setups

  Has reproduction · 84

  Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm via an evolutionarily conserved intronic enhancer

  e9.5 xenopus bulk rt-qpcr whole-mount

• A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.

  PMID 37936069 · PMC10629022 · BMC genomics · 2023 · 8 claims · 4 setups

  Has reproduction

  Hypersensitive response (HR) accompanied by systemic acquired resistance is the primary contributor to resistance against purple curl leaf disease in agave

  agave bulk wgcna qpcr

• An NSP2-MYB module orchestrates flavonoid biosynthesis and nodule symbiosis.

  PMID 41643674 · PMC7619063 · Current biology : CB · 2026 · 8 claims · 8 setups

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  NSP1 and NSP2 promote expression of flavonoid biosynthesis genes during nutrient starvation and rhizobial symbiosis in Medicago truncatula

  medicago nicotiana recombinant yeast rna-seq qpcr targeted

• Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

  PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups

  Has reproduction · 55

  352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples

  endometrial degs hub decidua microarray wgcna machine

• Glutamine-mediated crosstalk between M2 macrophages and tumor cells via the SLC38A5/FOXM1/CNIH4 axis promotes oral squamous cell carcinoma progression.

  PMID 41715179 · PMC13020291 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  Glutamine secretion from M2 macrophages to tumor cells via SLC38A5 is the core mCCC pathway upregulated in metastatic OSCC lesions compared to primary lesions.

  oscc epithelial tcga-oscc hsc-3 scrna-seq hdwgcna bulk

• Uncovering the transcriptional landscape of estrogen-induced gonadal feminization in the Chinese giant salamander.

  PMID 41808025 · PMC13085422 · BMC genomics · 2026 · 8 claims · 7 setups

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  E2 exposure induces male-to-female gonadal sex reversal in CGS, confirmed by histological evidence across developmental stages.

  gonadal tail-tip deg candidate rna-seq histology rt-qpcr

• Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

  PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

  meta-geo tcga-blca bca genomics unsupervised lasso weighted

• LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.

  PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 49

  LRP1 is a hub gene with the highest diagnostic performance among 30 candidate hub genes identified by machine learning

  ectopic geo gse5108 training microarray wgcna machine

• Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.

  PMID 40945691 · PMC12506565 · Molecular metabolism · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  snRNA-seq of murine BAT identifies seven distinct brown adipocyte subtypes with distinct metabolic profiles, part of a 21-cell-type atlas.

  interscapular ibat bat single-nucleus qpcr western

• Combinatory differentiation of human induced pluripotent stem cells generates functional thymic epithelium driving dendritic cell and CD4/CD8 T cell development.

  PMID 41577697 · PMC12932823 · Nature communications · 2026 · 8 claims · 6 setups

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  DOE-based multifactorial screening combined with bulk RNA-seq comparison to scRNA-seq pharyngeal atlases identifies signaling factors that optimize iPSc differentiation toward thymic epithelial progenitors (TEPs)

  ipsc embryonic ipsc-derived bulk scrna-seq qpcr

• XAP5 CIRCADIAN TIMEKEEPER coordinates circadian rhythms and anthocyanin biosynthesis independently of splicing.

  PMID 42014049 · PMC13227948 · Plant physiology · 2026 · 8 claims · 5 setups

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  XCT and PRP19 antagonistically regulate circadian period length through splicing-independent mechanisms

  arabidopsis computational luciferase rna-seq gene

• Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.

  PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups

  Has reproduction · 86

  RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.

  peripheral demrnas blood thp-1 rna-seq annotation wgcna