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).

• Autoencoder Networks Decipher the Association between Lung Cancer and Alzheimer's Disease.

  PMID 36518809 · PMC9744611 · Computational intelligence and neuroscience · 2022 · 7 claims · 6 setups

  Has reproduction · 74

  Autoencoder networks based on 266 shared DEGs reveal a comorbidity (positive) relationship between Alzheimer's disease and lung cancer.

  brain lung integrated shared microarray differential autoencoder

• 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

• From genomics to chemical genomics: new developments in KEGG.

  PMID 16381885 · PMC1347464 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  KEGG BRITE has been formally added as a fourth main KEGG database to establish a logical foundation for functional interpretation and pathway reconstruction.

  enzymatic substrate kegg complete chemical number ortholog

• A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

  PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

  Full-text index only

  Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

  genes hela proteins worm co-expression quantitative functional

• KEGG for linking genomes to life and the environment.

  PMID 18077471 · PMC2238879 · Nucleic acids research · 2008 · 8 claims · 4 setups

  Full-text index only

  KEGG provides a reference knowledge base for linking genomes to life via PATHWAY mapping and to the environment via BRITE mapping.

  protein-coding newly microarray kegg sequence computational glycan

• 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

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  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

• Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.

  PMID 38491422 · PMC10943865 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 5 setups

  Full-text index only

  The host genome's influence on the functional rumen microbiome contributes to temporal variation in average daily gain (ADG1-ADG4) across finishing months in beef cattle.

  rumen blood beef metagenome snp longitudinal

• 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

• miRGator: an integrated system for functional annotation of microRNAs.

  PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

  genome predicted tissues organs computational functional mirna

• miR-4478 Accelerates Nucleus Pulposus Cells Apoptosis Induced by Oxidative Stress by Targeting MTH1.

  PMID 36130054 · PMC9897280 · Spine · 2023 · 7 claims · 8 setups

  Has reproduction · 100

  miR-4478 is upregulated in nucleus pulposus tissues from IVDD patients and is degeneration-degree-associated

  annulus tissues npcs mirna quantitative fluorescence

• 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

• 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

• 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

• MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

  PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups

  Has reproduction · 24

  MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics

  environmental quality-filtered assembled predicted metagenomic metagenome gene

• 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

• A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

  PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups

  Full-text index only

  A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.

  kidney same identified additional microarray significance fisher's

• Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

  PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 7 claims · 8 setups

  Has reproduction · 91

  175 conserved and 83 novel miRNAs were identified mainly in one bud and two tender leaves of tea plant via small RNA sequencing combined with genome survey data

  camellia sinensis small genome mirna

• 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

• Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

  PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 20

  AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats

  ipf common key rats microarray network protein-protein

• Machine learning algorithm predicts fibrosis-related blood diagnosis markers of intervertebral disc degeneration.

  PMID 37915003 · PMC10619283 · BMC medical genomics · 2023 · 7 claims · 7 setups

  Has reproduction · 68

  CEP120 and SPDL1 are fibrosis-related diagnostic genes for IDD, identified via a random forest model from 29 differentially expressed fibrosis-related genes

  blood gse150408 prediction pbmcs bulk machine roc