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).

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

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 6 claims · 4 setups

  Has reproduction · 66

  Low STAT3 expression in primary prostate cancer is associated with up-regulated OXPHOS and ribosomal biosynthesis at the transcriptomic level.

  prostate pca bulk reverse ssgsea

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining

• g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

  PMID 17478515 · PMC1933153 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  g:Profiler integrates four modules (g:Profiler core, g:Convert, g:Orth, g:Sorter) into a single cross-linked web tool for gene list analysis

  input 1000-bp microarray organisms functional transcription gene

• KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

  PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

  diffuse-type liver renal anaplastic differential proteomic proteomics

• Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments.

  PMID 32093613 · PMC7041296 · BMC genomics · 2020 · 7 claims · 3 setups

  Has reproduction · 62

  The Equivalent Change Index (ECI), a gene-level statistic ranging from -1 to 1, quantifies whether a gene was changed to the same (1) or completely opposite (-1) degree across two experiments relative to their controls.

  simulated white model simulation gene

• GeneTrail--advanced gene set enrichment analysis.

  PMID 17526521 · PMC1933132 · Nucleic acids research · 2007 · 8 claims · 2 setups

  Full-text index only

  GeneTrail is a comprehensive, easy-to-use web-based tool for gene set enrichment analysis supporting both Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA)

  example sorted over-representation gene

• Functional genomics of the pregnant uterus: from expectations to reality, a compilation of studies in the myometrium.

  PMID 17570164 · PMC1892061 · BMC pregnancy and childbirth · 2007 · 8 claims · 6 setups

  Full-text index only

  Differential expression of 118 genes across compiled myometrium studies could be distributed into 14 main KEGG pathways most representative of changes between NP, PTNIL, TNIL and TIL states

  myometrium compiled cdna oligonucleotide kegg

• Deconvoluting the 'omics' for organ transplantation.

  PMID 19644370 · PMC2993238 · Current opinion in organ transplantation · 2009 · 8 claims · 5 setups

  Full-text index only

  High-throughput 'omic' technologies (genomics, proteomics, metabolomics, antibiomics) can uncover novel biomarkers for acute rejection, chronic rejection, and operational tolerance without a priori pathway bias

  kidney sera peripheral microarray non-parametric antibiomics

• Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.

  PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 74

  540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed

  breast colorectal lung common microarray kegg protein-protein

• FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

  PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

  user-supplied gene predicted interactome gene kegg transcription

• 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

• Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.

  PMID 34143800 · PMC8213194 · PloS one · 2021 · 7 claims · 6 setups

  Has reproduction · 75

  306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified across three independent GEO datasets in EOC vs normal ovarian tissue.

  eoc overlapping tcga microarray kegg protein-protein

• 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 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

• Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

  PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

  heart degs dgat2 mitodegs microarray kegg protein-protein

• Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studies.

  PMID 41909810 · PMC13022592 · Frontiers in bioinformatics · 2026 · 8 claims · 4 setups

  Has reproduction · 56

  ChickpeaOmicsR is the first comprehensive/specialized R package integrating transcriptomic, genomic, and proteomic (RNA-seq, GWAS, PPI) data within a unified, reproducible framework and standardizing fragmented chickpea gene nomenclature.

  cicer chickpea icarda bulk gene protein-protein

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• The proteogenomic path towards biomarker discovery.

  PMID 18764911 · PMC2574627 · Pediatric transplantation · 2008 · 8 claims · 8 setups

  Full-text index only

  Serum creatinine is a widely used but non-ideal biomarker for renal transplant monitoring because it lacks specificity and sensitivity for graft injury

  renal urine breast chronic microarray immunoassay gel

• Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

  PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups

  Has reproduction · 86

  A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.

  known tnbc unique unknown gene machine term

• 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