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).

• 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

• Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

  PMID 35012625 · PMC8743438 · Genome biology · 2022 · 7 claims · 8 setups

  Has reproduction · 68

  GENEVA is a semi-automated, study-design-agnostic framework that mines large-scale public RNA-seq data to identify conditions modulating a gene of interest's expression

  gtex lncap heart breast bulk rna-seq meta-analysis

• TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.

  PMID 33705981 · PMC9403021 · Genomics, proteomics & bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 79

  TSUNAMI is a freely accessible web-based tool suite that mines gene co-expression network (GCN) modules from public (GEO, TCGA) or user-uploaded numerical omics data and performs downstream gene set enrichment analysis.

  gse17537 36th first gene circos survival

• SGCP: a spectral self-learning method for clustering genes in co-expression networks.

  PMID 38956463 · PMC11221046 · BMC bioinformatics · 2024 · 7 claims · 4 setups

  Has reproduction · 51

  SGCP, a spectral self-learning method, yields gene co-expression modules with higher GO enrichment than WGCNA, CoExpNets, and CEMiTool across 12 real gene expression datasets.

  real microarray rna-seq same gene dna-microarray rna-sequencing

• Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.

  PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 71

  LUAD samples cluster into IRG-high and IRG-low groups, with the IRG-high group showing significantly better survival and greater immune cell infiltration.

  luad geo degs immunotherapy-treated bulk weighted ppi

• 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 · 7 claims · 8 setups

  Has reproduction · 71

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

  bca meta-geo tcga-blca tcga bulk rna-seq somatic

• Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

  PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 7 claims · 8 setups

  Has reproduction · 59

  Eight gene modules linked to metastasis were identified via scored network analysis and validated through pathway databases.

  metastatic tcga-brca homo gse40622 gene bulk rt-pcr

• 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 · 7 claims · 8 setups

  Has reproduction · 49

  LRP1 is the top hub gene with the highest diagnostic performance for distinguishing ectopic from eutopic endometrium in EMS

  ectopic geo training gwas microarray wgcna machine

• DiRE: identifying distant regulatory elements of co-expressed genes.

  PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups

  Full-text index only

  DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures

  liver myod transgenic microarray tfbs enhancer

• Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.

  PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups

  Has reproduction · 80

  Combining WGCNA-derived hub genes with a VAE-derived 10-dimensional representation as features for an SVM classifier achieves high accuracy (0.9692) and AUC (0.9981) for colorectal cancer prediction.

  colorectal combined differentially crc microarray differential weighted

• AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

  PMID 27082953 · PMC4833304 · PLoS computational biology · 2016 · 7 claims · 4 setups

  Has reproduction · 88

  Sample-sample correlation of transcript abundances is trivially high regardless of condition and gives misleading estimates of the replicability of conditional (differential) variation in expression.

  encode liver bulk rna-seq meta-analysis

• Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

  PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 83

  Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs

  afb1 breast training candidate computational bulk weighted

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor

• Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.

  PMID 41953002 · PMC13053772 · iScience · 2026 · 7 claims · 8 setups

  Has reproduction · 78

  An integrated framework of bioinformatics, machine learning, and ΔG clustering can prioritize PAHs for AD-associated neurotoxicity.

  proteins microarray ad-associated pahs target differential wgcna

• Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues.

  PMID 34056582 · PMC8155268 · Frontiers in artificial intelligence · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  MCF-7 cell lines and human breast cancer tissues share only minimal similarity in biological processes, though fundamental functions such as cell cycle are conserved

  mcf-7 breast wgcna top bulk microarray weighted

• 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

• Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

  PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

  Full-text index only

  MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

  hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical