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).

• 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 hub genes and VAE 10-dimensional representation as features for an SVM classifier achieves high accuracy in predicting CRC

  colorectal same combined meturquoise microarray differential batch

• Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.

  PMID 34532385 · PMC8421925 · Annals of translational medicine · 2021 · 8 claims · 7 setups

  Has reproduction · 44

  The brown co-expression module (775 genes) is the module most significantly associated with the chronic stage of SCI

  spinal brown sci microarray functional protein-protein

• 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

  Full-text index only

  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

• 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

  Full-text index only

  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

• Enhanced Bioremediation Potential of Shewanella decolorationis RNA Polymerase Mutants and Evidence for Novel Azo Dye Biodegradation Pathways.

  PMID 35391736 · PMC8981235 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

  Has reproduction · 80

  Unbiased RNAP (rpoB) mutation screening via rifampicin resistance is an effective method to obtain bacterial mutants with enhanced bioremediation activity

  shewanella decolorationis rifampicin pcr minimum

• Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.

  PMID 35901050 · PMC9333241 · PloS one · 2022 · 7 claims · 7 setups

  Has reproduction · 55

  Several WGCNA gene co-expression modules are significantly associated with both LVEF and the DCM phenotype in heart failure patients.

  heart degs gene genes bulk gene kegg

• Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.

  PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.

  cervical als top yeast bulk stratified protein-protein

• Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.

  PMID 18986552 · PMC2625353 · BMC systems biology · 2008 · 8 claims · 6 setups

  Full-text index only

  Integrated WGCNA (IWGCNA), which adds genetic marker-based causality testing to standard WGCNA, can identify a disease-related module and its causal drivers

  cfs most candidate second microarray snp weighted

• Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.

  PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 6 claims · 8 setups

  Has reproduction · 71

  109 shared genes were identified between HIV-1- and PAH-associated WGCNA modules

  pbmc shared hub pbmcs weighted kegg differential

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• Screening of Diagnostic Biomarkers and Immune Infiltration Characteristics Linking Rheumatoid Arthritis and Rosacea Based on Bioinformatics Analysis.

  PMID 39104909 · PMC11299729 · Journal of inflammation research · 2024 · 8 claims · 8 setups

  Has reproduction · 48

  277 co-expressed DEGs shared between RA and rosacea are enriched in immune processes and chemokine-mediated signaling pathways

  synovial rosacea co-expressed serum microarray weighted protein-protein

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

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

  Full-text index only

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

  left mus combined heart microarray weighted bulk

• 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

• Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.

  PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 8 claims · 8 setups

  Has reproduction · 80

  A neutrophil-related co-expression gene module (blue module) is significantly associated with aSAH occurrence

  peripheral genes overlapping neutrophil-related microarray weighted kegg

• A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

  PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

  Has reproduction · 62

  Inter-specific differences in vertical distribution/microhabitat preference are associated with distinct dynamics of gene expression during dehydration and rehydration phases

  hymenophyllum caudiculatum annotated rna-seq chlorophyll relative

• 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

  Full-text index only

  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 novel 10 immune-related genes signature as a prognostic biomarker panel for gastric cancer.

  PMID 34382341 · PMC8446556 · Cancer medicine · 2021 · 8 claims · 8 setups

  Has reproduction

  A 10-IRG prognostic signature (BMPR1B, GHR, IL11RA, INHBB, NPR3, OBP2A, PTN, R3HDML, TAC1, TPM2) predicts overall survival in gastric cancer.

  gastric tcga-stad overlapping candidate microarray gene rna-seq

• STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 8 claims · 6 setups

  Has reproduction · 66

  Low STAT3 expression in primary PCa is associated with increased OXPHOS and ribosomal biosynthesis at the transcriptomic level

  prostate bulk weighted reverse

• Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

  PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups

  Has reproduction · 49

  ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC

  ptc degs key bulk kegg weighted

• 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 · 6 setups

  Has reproduction · 92

  MCF-7 cell lines and human breast cancer tissues show only minimal similarity in biological processes, though some fundamental functions like cell cycle are conserved.

  mcf-7 breast wgcna-derived top bulk microarray rsem-normalized