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).

• 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

• 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

• Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.

  PMID 37883426 · PMC10602290 · PloS one · 2023 · 6 claims · 7 setups

  Has reproduction · 97

  TAA/TAV pathogenesis is more associated with immune-related gene expression than TAA/BAV, with two WGCNA gene modules (brown and blue) enriched for immune functions.

  aortic brown genes training wgcna biological gsva

• 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

• 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

• 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

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

  PMID 35901050 · PMC9333241 · PloS one · 2022 · 5 claims · 8 setups

  Has reproduction · 55

  Several co-expressed gene modules are significantly associated with left ventricle ejection fraction (LVEF) and the DCM phenotype, enriched in fibrosis-related, small molecule transporting-related, and immune response-related pathways.

  heart degs gene rna-seq bulk differential gene

• Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.

  PMID 37415981 · PMC10320004 · Frontiers in immunology · 2023 · 7 claims · 8 setups

  Has reproduction · 58

  EAF1, SDCBP and RNF19B are common genetic characteristics (hub genes) shared by RA and MDD

  pbmc intersected candidate wgcna differential 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

• 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

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

  PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 7 claims · 7 setups

  Has reproduction · 71

  HIV-1 and PAH share 109 co-expressed genes primarily enriched in type I interferon (IFN) pathways.

  pbmc shared gene microarray kegg

• Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity.

  PMID 33837217 · PMC8035321 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 68

  MOCCI (encoded by C15ORF48) is a mito-SEP upregulated during inflammation and infection that promotes host-protective resolution

  aortic failing colon hek293t ribo-seq wgcna-gsea gene

• Exploration of the shared diagnostic genes and molecular mechanism between obesity and atherosclerosis via bioinformatic analysis.

  PMID 39825072 · PMC11742665 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 76

  56 shared genes with consistent expression trend were identified between OB and AS by intersecting WGCNA key module genes with DEGs

  obesity atherosclerosis differential wgcna lasso

• 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

• Exploring the key genetic association between chronic pancreatitis and pancreatic ductal adenocarcinoma through integrated bioinformatics.

  PMID 37501719 · PMC10369079 · Frontiers in genetics · 2023 · 6 claims · 7 setups

  Has reproduction · 91

  CEL (carboxyl ester lipase) is the real hub gene shared between CP and PDAC and is markedly downregulated in PDAC

  pancreatic gse143754 pdac tcga microarray wgcna differential

• Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

  PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 96

  A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.

  gastric gene scrna-seq tcga single-cell wgcna cell-cell

• 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

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

  PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups

  Has reproduction · 80

  Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.

  peripheral overlapping asah drug-treatment microarray wgcna ppi

• Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies.

  PMID 34107850 · PMC8806433 · Bioengineered · 2021 · 6 claims · 6 setups

  Has reproduction · 55

  TYR, TYRP1, DCT and LARP7 are biomarkers associated with vitiligo

  vitiligo merged robust gse90880 gene robust kegg

• 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