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 1.1k

System / cell line: analysis ✕ Assay: expression ✕ Clear

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
The genetics of regulatory variation in the human genome.

PMID 16004727 · PMC3525257 · Human genomics · 2005 · 8 claims · 7 setups

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Naturally-occurring gene expression variation among individuals is common across species (yeast, Drosophila, mouse, fish, maize, primates, humans) and has a significant genetic component.

ceph immortalised lymphoblastoid individuals reporter allelic microarray
Computational analysis of the synergy among multiple interacting genes.

PMID 17299419 · PMC1828751 · Molecular systems biology · 2007 · 8 claims · 3 setups

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Multivariate synergy of a set of factors with respect to a phenotype can be defined via the maximum-information partition, i.e., comparing the mutual information of the full set to the best achievable sum of mutual information over any partition into disjoint subsets.

healthy biological hypothetical gene snp illustrative
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

PMID 35012625 · PMC8743438 · Genome biology · 2022 · 7 claims · 8 setups

Has reproduction · 68

GENEVA is a semi-automated, study-design-agnostic framework that mines large-scale public RNA-seq data to identify conditions modulating a gene of interest's expression

gtex lncap heart breast bulk rna-seq meta-analysis
Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.

PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 7 claims · 5 setups

Has reproduction · 62

A DNN model using the top 34 betweenness-centrality-ranked hub genes predicts bone metastasis with AUC of 92.11% on the GEO validation data.

breast degs geo tcga gene protein-protein machine
The genomic analysis of lactic acidosis and acidosis response in human cancers.

PMID 19057672 · PMC2585811 · PLoS genetics · 2008 · 8 claims · 8 setups

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Lactic acidosis and hypoxia induce largely distinct gene expression programs in HMECs, with lactic acidosis producing a much larger and more dramatic response

mammary hmec gene breast gene real-time bayesian
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
Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

PMID 18003658 · PMC2248751 · Nucleic acids research · 2008 · 8 claims · 8 setups

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p110 CUX1 is recruited to promoters of cell cycle-related target genes preferentially during S phase

hela hs578t nih3t3 genomic chap-chip conventional scanning
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

PMID 16381948 · PMC1347397 · Nucleic acids research · 2006 · 6 claims · 2 setups

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CAGE Basic and Analysis Databases together form a comprehensive resource for promoter analysis using CAGE tag data from human and mouse

tested cage race
Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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Current syndromic disease classification lacks specificity despite historically serving clinicians well

prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene
Widespread ectopic expression of olfactory receptor genes.

PMID 16716209 · PMC1508154 · BMC genomics · 2006 · 8 claims · 6 setups

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OR genes show widespread, locus-dependent, heterogeneous ectopic expression across dozens of non-olfactory human and mouse tissues

tissues olfactory intact probesets microarray est custom
Reusable building blocks in biological systems.

PMID 30958230 · PMC6303794 · Journal of the Royal Society, Interface · 2018 · 8 claims · 4 setups

Has reproduction · 82

Biological systems can be decomposed into phenotypic building blocks (PBBs) via k-maximally reusable decompositions (k-MRD) that maximize average reusability across conditions.

tissues conditions randomized est-based mirna randomization
Relative impact of nucleotide and copy number variation on gene expression phenotypes.

PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

lymphoblastoid same computational subset gene snp array
Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

PMID 17598913 · PMC1929078 · BMC genomics · 2007 · 8 claims · 4 setups

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Standard Affymetrix expression GeneChips (MOE430, HG-U133) contain probe sets that detect natural antisense transcripts (NATs)

moe430 pooled organs probe strand-specific microarray
Similarities and differences in genome-wide expression data of six organisms.

PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

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Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental
Asthma investigators begin to reap the fruits of genomics.

PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups

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Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.

monkey models lung inbred cdna oligonucleotide northern
Can we find the genes involved in complex traits?

PMID 15461809 · PMC545590 · Genome biology · 2004 · 8 claims · 8 setups

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Large regions of the mouse genome exist in linkage disequilibrium (LD), including a 40 Mb region on the X chromosome, reflecting selection against recombination to preserve allelic combinations.

inbred strains 000-strain recombinant snp expression eqtl
Metatranscriptomics of the human oral microbiome during health and disease.

PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups

Has reproduction · 62

Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.

patient-matched subset health rna-seq rrna comparison metatranscriptomics
Extending Asia Pacific bioinformatics into new realms in the "-omics" era.

PMID 19958472 · PMC2788361 · BMC genomics · 2009 · 8 claims · 6 setups

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88 full paper submissions were peer-reviewed for InCoB2009, with 49 shortlisted for oral presentation and 34 accepted into this BMC Genomics supplement, reflecting an overall acceptance rate of 50% across venues.

nhe1 cancer mammalian bovine computational microarray quantile
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

Has reproduction · 86

CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

tissues predicted tss-enhancer cattle cage extraction coexpression

Experiments

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.

The genetics of regulatory variation in the human genome.

Computational analysis of the synergy among multiple interacting genes.

Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.

The genomic analysis of lactic acidosis and acidosis response in human cancers.

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

Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

Widespread ectopic expression of olfactory receptor genes.

Reusable building blocks in biological systems.

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

Similarities and differences in genome-wide expression data of six organisms.

Asthma investigators begin to reap the fruits of genomics.

Can we find the genes involved in complex traits?

Metatranscriptomics of the human oral microbiome during health and disease.

Extending Asia Pacific bioinformatics into new realms in the "-omics" era.

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.