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).
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Has reproduction · 100
Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome.
PMID 34561431 · PMC8463674 · Nature communications · 2021 · 8 claims · 7 setups
revTWMR, a reverse transcriptome-wide Mendelian Randomization approach integrating GWAS and whole-blood trans-eQTL summary statistics, is proposed to estimate the causal effect of a phenotype on gene expression.
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Has reproduction · 70
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).
PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups
AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella
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Has reproduction · 60
Transcriptome maps of general eukaryotic RNA degradation factors.
PMID 31135339 · PMC6570525 · eLife · 2019 · 8 claims · 4 setups
Transcriptome-wide binding profiles of 30 general RNA degradation factors in S. cerevisiae reveal their distribution across different RNA classes.
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Has reproduction · 71
Transcriptome and machine learning analysis of the impact of COVID-19 on mitochondria and multiorgan damage.
PMID 38295140 · PMC10830027 · PloS one · 2024 · 6 claims · 7 setups
Potential cardiac, hepatic, and renal impairments in COVID-19 are associated with ACE2, inflammatory cytokine storms, and mitochondrial pathways.
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Has reproduction · 85
Exploring microproteins from various model organisms using the mip-mining database.
PMID 37919660 · PMC10623795 · BMC genomics · 2023 · 5 claims · 4 setups
Mip-mining is a database of 336 curated RNA-seq datasets from 8626 samples across nine species, built specifically to explore microprotein functions under stress and disease conditions
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Has reproduction · 50
STAT1 and IL-7 as potential diagnostic biomarkers for distinguishing high-grade from low-grade serous ovarian cancer: a multi-cohort analysis.
PMID 42058211 · PMC13120972 · Frontiers in immunology · 2026 · 7 claims · 6 setups
STAT1 and IL-7 are differentially expressed immune-related genes that can distinguish HGSOC from LGSOC and may serve as ancillary diagnostic biomarkers.
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Has reproduction · 73
Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.
PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups
De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp
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Has reproduction · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases
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Has reproduction · 74
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups
Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.
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Has reproduction · 82
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.
PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups
An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.
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Has reproduction · 27
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.
PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups
A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.
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Transcriptome and proteome expressions involved in insulin resistance in muscle and activated T-lymphocytes of patients with type 2 diabetes.
PMID 18267303 · PMC5054231 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups
Gene expression of INSR, VDR, IDE, Akt, IRS-1, IRS-2, GLUT4, and glycolytic pathway enzymes is decreased at least 50% in T2DM muscle and activated T-cells versus non-diabetic controls
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A comprehensive modular map of molecular interactions in RB/E2F pathway.
PMID 18319725 · PMC2290939 · Molecular systems biology · 2008 · 8 claims · 4 setups
A comprehensive, curated map of RB/E2F pathway molecular interactions was built using SBGN notation in CellDesigner and converted to BioPAX 2.0 format
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Has reproduction · 76
A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.
PMID 28642491 · PMC5481429 · Scientific reports · 2017 · 6 claims · 8 setups
Hnf4a is a major transcriptional regulator of Dnajc22.
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Has reproduction · 51
A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.
PMID 39280688 · PMC11399026 · Translational andrology and urology · 2024 · 8 claims · 8 setups
An Enet (alpha=0.4) machine-learning algorithm built from 10 platelet-related genes yields the optimal platelet-related signature (PRS) for bladder cancer prognosis, with average C-index 0.73
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Has reproduction · 93
Under the Shadow: Old-biased Genes Are Subject to Weak Purifying Selection at Both the Tissue- and Cell Type-Specific Levels.
PMID 41092135 · PMC12569596 · Genome biology and evolution · 2025 · 8 claims · 6 setups
Age-related decrease in transcriptome conservation (ADICT) is commonly found in ageing tissues of nonmammalian species (chicken brain, killifish liver and skin, fruit fly brain).
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Has reproduction · 49
LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.
PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 7 claims · 8 setups
LRP1 is the top hub gene with the highest diagnostic performance for distinguishing ectopic from eutopic endometrium in EMS
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Has reproduction · 54
Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.
PMID 27355630 · PMC4927094 · PloS one · 2016 · 8 claims · 8 setups
In Cstb-/- microglia, 184 genes were differentially expressed relative to control, of which 33 were identified by both microarray and RNA-seq.
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Has reproduction · 87
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.
PMID 34072576 · PMC8227486 · Genes · 2021 · 6 claims · 8 setups
A consensus transcriptome assembled by combining reads from five independent studies is the most complete E. gracilis transcriptome released to date, outperforming the two previously available transcriptomes (GEFR01 and GDJR01).
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Has reproduction · 64
Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.
PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups
A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs