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).

Publications 1.3k Datasets 392.5k Experiments 17

System / cell line: healthy ✕ Assay: correlated ✕ Clear

Proteomics: characterizing the cogs in the machinery of life.

PMID 14630521 · PMC1241753 · Environmental health perspectives · 2003 · 8 claims · 5 setups

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Protein expression patterns in blood serum, detected via SELDI-TOF mass spectrometry and analyzed with a genetic algorithm, can distinguish ovarian cancer patients from healthy individuals with very high sensitivity and specificity.

blood lung hemoglobin proteins seldi-tof proteome tandem
Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

PMID 15601541 · PMC3525069 · Human genomics · 2004 · 8 claims · 6 setups

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DNA microarray gene expression profiling generates robust molecular classifications for many tumour types (brain, breast, colon, gastric, kidney, leukaemia, lymphoma, lung, melanoma, ovary, prostate, etc.)

breast sars serum tumour microarray custom mass
Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

Has reproduction · 71

TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

blood cynomolgus external gene differential principal
MIRit: an integrative R framework for the identification of impaired miRNA-mRNA regulatory networks in complex diseases.

PMID 41800385 · PMC12961272 · Bioinformatics advances · 2026 · 8 claims · 5 setups

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MIRit is a comprehensive, open-source R/Bioconductor framework for integrative miRNA–mRNA analysis that supports both paired and unpaired datasets using statistically appropriate methods.

myocardial ccrcc brodmann synthetic mirna-seq microarray small
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
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

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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
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

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90 interacting genes were identified at the intersection of AAA DEGs and periodontitis WGCNA module genes

abdominal gingival overlapping interacting microarray weighted kegg
Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

PMID 41564862 · PMC12866174 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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A 19-factor cancer-immunoinstructive secretory signature (CISS) is present across multiple human cancers and correlates with pro-tumorigenic tumor microenvironments and poor patient survival.

pancreatic kpc pdac tcga-paad rna-seq bulk proteomics
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

170 unique human AFB1 targets were identified by merging ChEMBL, SwissTargetPrediction, and PharmMapper predictions

afb1 breast training candidate computational bulk weighted
Multi-scale integrative analyses identify THBS2(+) cancer-associated fibroblasts as a key orchestrator promoting aggressiveness in early-stage lung adenocarcinoma.

PMID 35547750 · PMC9065207 · Theranostics · 2022 · 8 claims · 8 setups

Has reproduction · 68

THBS2 is a tumor size-independent biomarker that robustly predicts post-surgical OS and RFS in multiple independent early-stage LUAD cohorts

tcga paired thbs2+ scrna-seq wgcna scrna-seq gsea
Smoking promotes colorectal cancer via the CKAP2L/AREG axis.

PMID 41823522 · PMC13038336 · International journal of oncology · 2026 · 8 claims · 8 setups

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Smoking is positively associated with CRC risk, confirmed by both cross-sectional (NHANES) and Mendelian randomization analyses

participants european crc hct116 cross-sectional two-sample single-cell
Machine learning algorithm predicts fibrosis-related blood diagnosis markers of intervertebral disc degeneration.

PMID 37915003 · PMC10619283 · BMC medical genomics · 2023 · 8 claims · 7 setups

Has reproduction · 68

CEP120 and SPDL1 were identified as diagnostic genes for IDD using a random forest model

blood gse150408 cep120 pbmcs bulk machine single-sample
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups

Has reproduction · 78

A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors

hcc-associated hcc malignant cd8+ single-cell bulk metabolomics
Usefulness of cancer-testis antigens as biomarkers for the diagnosis and treatment of hepatocellular carcinoma.

PMID 17244360 · PMC1797003 · Journal of translational medicine · 2007 · 8 claims · 8 setups

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HCC is a highly heterogeneous, non-linear disease driven by complex, multi-stage genetic and environmental alterations

hcc serum sera peripheral serum expression enzyme
Reprogramming of stroma-derived chemokine networks drives the loss of tissue organization in nodal B cell lymphoma.

PMID 41882179 · PMC13035477 · Nature cancer · 2026 · 8 claims · 8 setups

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LN-resident stromal cells (FRCs, BECs, LECs) drive chemokine-based lymphocyte zonation, and disruption of this system underlies the loss of tissue organization in nodal B cell lymphoma

rln healthy bulk fl-ln scrna-seq multiplex bulk
Secreted phospholipase PLA2G5 acts as a hemolytic factor in sepsis.

PMID 42065235 · PMC13132393 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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Pla2g5 gene expression is induced in the colon and small intestine during LPS-induced endotoxemia and CLP-induced sepsis in mice

colon mice serum bone whole-mount rna-seq survival
ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

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Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

ductal same sporadic paired cdna quantitative genotyping

Experiments

Proteomics: characterizing the cogs in the machinery of life.

Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

MIRit: an integrative R framework for the identification of impaired miRNA-mRNA regulatory networks in complex diseases.

Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

Exploration of effective biomarkers for venous thrombosis embolism in Behçet's disease based on comprehensive bioinformatics analysis.

Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

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

Multi-scale integrative analyses identify THBS2(+) cancer-associated fibroblasts as a key orchestrator promoting aggressiveness in early-stage lung adenocarcinoma.

Smoking promotes colorectal cancer via the CKAP2L/AREG axis.

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

Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

Usefulness of cancer-testis antigens as biomarkers for the diagnosis and treatment of hepatocellular carcinoma.

Reprogramming of stroma-derived chemokine networks drives the loss of tissue organization in nodal B cell lymphoma.

Secreted phospholipase PLA2G5 acts as a hemolytic factor in sepsis.

ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.