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 106

System / cell line: microarray ✕ Assay: functional ✕ Clear

Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.

PMID 19943934 · PMC2794290 · BMC cancer · 2009 · 8 claims · 5 setups

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Hundreds of genes differentiate GISTs according to KIT versus PDGFRA mutation and expression status, despite no discriminative profile for clinical/pathological parameters.

frozen genomic formalin-fixed differentially microarray sequencing quantitative
Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups

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Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions

normal genome-wide same omim microarray sage computational
Towards precise classification of cancers based on robust gene functional expression profiles.

PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

nci60 lymphoma fep go-annotated cdna recursive hypergeometric
Expanding the vision of environmental health at UNC-CH.

PMID 15248304 · PMC1247395 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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Human breast tumors arise from at least two distinct cell types, basal and luminal epithelial, with different clinical behavior

breast chinese carolina rodent microarray functional genetic
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

user-supplied ranked gene fasta-formatted functional gene novo
The integrated world of functional genomics.

PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

cerevisiae sequenced elegans drosophila chromatin integration comparative
Web-based resources for comparative genomics.

PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood
Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

PMID 17888167 · PMC2082044 · BMC genomics · 2007 · 8 claims · 6 setups

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A proposed coupled two-way clustering (CTWC/SPC) method combined with a GO-based functional concept consistency score can identify compact, robust gene subsets that define clinically meaningful DLBCL subtypes

dlbcl identified microarray oligonucleotide coupled
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
A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

PMID 16423292 · PMC1382217 · BMC genomics · 2006 · 7 claims · 6 setups

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Expression context is largely conserved between orthologs across four eukaryote species.

elegans pairwise orthologs cerevisiae microarray ortholog functional
Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

PMID 17880677 · PMC2375035 · Genome biology · 2007 · 7 claims · 8 setups

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Combining pairs of omics evidence types into two-dimensional 'evidence landscapes' allows regions to be identified that specifically and purely predict either physical or metabolic protein interactions

saccharomyces correlated chip-chip gene
Genomic expression during human myelopoiesis.

PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups

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An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.

myeloid same cd34+ gene microarray unsupervised sam
A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups

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Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units

pbmc genes monocytes original microarray literature stimulation
A taxonomy of epithelial human cancer and their metastases.

PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

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Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

epithelial tumor metastatic breast microarray gene fisher
CLEAN: CLustering Enrichment ANalysis.

PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

four breast combined hierarchical cluster csimm-based
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
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
Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.

PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups

Has reproduction · 83

188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways

blood degs peripheral hub microarray kegg cibersort
Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension.

PMID 36277786 · PMC9582241 · Frontiers in cardiovascular medicine · 2022 · 7 claims · 8 setups

Has reproduction · 73

FBXW4 and 13 other genes are uniquely enriched in the general hypertension group

peripheral white four gse75360 microarray gene weighted
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

Experiments

Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.

Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

Towards precise classification of cancers based on robust gene functional expression profiles.

Expanding the vision of environmental health at UNC-CH.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

The integrated world of functional genomics.

Web-based resources for comparative genomics.

Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

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

A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

Genomic expression during human myelopoiesis.

A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

A taxonomy of epithelial human cancer and their metastases.

CLEAN: CLustering Enrichment ANalysis.

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

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

Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.

Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension.

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