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 1.2k

Assay: gene-expression ✕ Clear

Functional genomics of early cortex patterning.

PMID 16515721 · PMC1431711 · Genome biology · 2006 · 7 claims · 6 setups

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The neocortical protomap is established as continuous rostro-caudal gradients of gene expression in progenitor cells, not discrete compartments

neocortex embryonic fgfr1-mutant cortex oligonucleotide situ microarray
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
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
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates.

PMID 17986453 · PMC2238949 · Nucleic acids research · 2008 · 8 claims · 5 setups

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TranspoGene catalogs TEs within protein-coding genes of seven species (human, mouse, chicken, zebrafish, fruit fly, nematode, sea squirt), classified as proximal promoter, exonized, exonic, or intronic TEs.

chicken normal tes genes genomic exon microrna
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

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A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

breast computational array-cgh gene bac
Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

PMID 17868458 · PMC2375029 · Genome biology · 2007 · 8 claims · 8 setups

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Co-culture of certain breast cancer cell lines with stromal fibroblasts induces interferon-response genes (IRGs) in a subset of cancer cells

mda-mb231 epithelial breast early-stage cdna quantitative facs
Comparative genomic analysis of prion genes.

PMID 17199895 · PMC1781936 · BMC genomics · 2007 · 8 claims · 8 setups

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SPRN and PRNP homologues are present in all vertebrates, whereas PRND is restricted to tetrapods and PRNT is restricted to primates

vertebrate multi-tissue aligned sprn comparative gene cdna
Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.

PMID 19109909 · PMC2630178 · Neuron · 2008 · 8 claims · 8 setups

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MEF2 directly regulates a genome-wide program of 182 activity-dependent target genes in hippocampal neurons

e18 hippocampal forebrain profiling rt-qpcr chip-chip
Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

PMID 18930150 · PMC2774125 · Methods (San Diego, Calif.) · 2008 · 8 claims · 8 setups

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Data integration of multiple functional genomics datasets effectively predicts mitochondrial gene function and prioritizes candidate mitochondrial disease genes.

saccharomyces higher yeast mitochondria genome-wide rnai gene
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

PMID 18660809 · PMC2652037 · Nature genetics · 2008 · 7 claims · 8 setups

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Evolution in the Typhi population is characterized by ongoing loss of gene function (pseudogene accumulation) rather than gain of function or diversifying selection.

salmonella sequenced typhi whole-genome snp-based selection
CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

neuroblastoma nlf athymic methylation-specific quantitative soft
Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.

PMID 18560825 · PMC2493868 · Immunogenetics · 2008 · 8 claims · 8 setups

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Neither transcriptional profiling alone nor genetic linkage analysis alone has been an effective approach to identify genes or gene networks that specify stemness or initiate differentiation/lineage specification.

escs fibroblasts hematopoietic bxd transcriptional forced long-term
Divide and conquer: progress in the molecular stratification of cancer.

PMID 19718393 · PMC2730607 · Yonsei medical journal · 2009 · 8 claims · 8 setups

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Cancers exhibit significant clinical, histopathologic, and molecular heterogeneity between individual patients

breast nsclc colon early-stage immunohistochemistry gene comparative
The molecular characterization and clinical management of multiple myeloma in the post-genome era.

PMID 19657360 · PMC3686133 · Leukemia · 2009 · 8 claims · 8 setups

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GEP identifies distinct molecular subgroups of MM associated with differing clinical features and survival outcomes

myeloma cd138-immunomagnetically plasma bone-marrow filter-based gene-expression targeted
Brain progranulin expression in GRN-associated frontotemporal lobar degeneration.

PMID 19649643 · PMC3104467 · Acta neuropathologica · 2010 · 8 claims · 8 setups

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GRN transcript haploinsufficiency, previously shown in blood-derived cells, does not hold in most brain regions of GRN mutation carriers

peripheral postmortem hek293 qrt-pcr microarray rt-pcr
Pharmacogenomic screening identifies and repurposes leucovorin and dyclonine as pro-oligodendrogenic compounds in brain repair.

PMID 39537633 · PMC11561360 · Nature communications · 2024 · 8 claims · 8 setups

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A pharmacogenomic scoring strategy (OligoScore) combining transcriptomic signatures and curated oligodendrogenesis gene sets identifies compounds with pro-oligodendrogenic transcriptional activity

brain neonatal gene cerebellar bulk transcriptomic pharmacogenomic
Characterization of Human Genes Modulated by Porphyromonas gingivalis Highlights the Ribosome, Hypothalamus, and Cholinergic Neurons.

PMID 34194426 · PMC8236716 · Frontiers in immunology · 2021 · 8 claims · 8 setups

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Genes in the SRP-dependent cotranslational protein targeting to membrane (ER translocation) pathway and ribosomal subunit genes are strongly and specifically enriched for arginine and lysine residues, suggesting high susceptibility to gingipain cleavage.

protein-coding coli recombinant postmortem proteome-wide gene gingipain
Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.

PMID 41839849 · PMC12992920 · Nature communications · 2026 · 8 claims · 8 setups

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274,682 enhancers and 25,975 promoters were characterized across 24 tissues from an adult female sheep using ChIP-seq, ATAC-seq, CAGE-seq, RRBS, WGBS, and RNA-seq.

tissues sheep pig chip-seq atac-seq cage-seq
Loss of long-range co-expression is a common feature in cancer.

PMID 41935098 · PMC13247121 · NPJ systems biology and applications · 2026 · 8 claims · 7 setups

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In cancer, the strongest co-expressed gene pairs (top MI values) are predominantly intra-chromosomal, unlike in normal tissue.

tissues same bladder cancer bulk differential bootstrap
Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

PMID 42054377 · PMC13127959 · PloS one · 2026 · 8 claims · 7 setups

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Integrating prothoracic ganglion RNAseq data with the draft genome refines gene predictions, adding 3,868 novel genes and 9,172 new transcript isoforms (including non-coding transcripts)

bimaculatus prothoracic differentially gbig rna-seq genome differential

Experiments

Functional genomics of early cortex patterning.

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

Metatranscriptomics of the human oral microbiome during health and disease.

TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates.

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

Comparative genomic analysis of prion genes.

Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.

Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.

Divide and conquer: progress in the molecular stratification of cancer.

The molecular characterization and clinical management of multiple myeloma in the post-genome era.

Brain progranulin expression in GRN-associated frontotemporal lobar degeneration.

Pharmacogenomic screening identifies and repurposes leucovorin and dyclonine as pro-oligodendrogenic compounds in brain repair.

Characterization of Human Genes Modulated by Porphyromonas gingivalis Highlights the Ribosome, Hypothalamus, and Cholinergic Neurons.

Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.

Loss of long-range co-expression is a common feature in cancer.

Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.