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).

• Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.

  PMID 37948380 · PMC10637681 · PloS one · 2023 · 8 claims · 8 setups

  Has reproduction · 90

  Stemness-related genes ORC1L, KIF20A, and DLGAP5 are upregulated in LUAD and correlate with altered immune cell infiltration (Th2, MDSC, HSC) and reduced patient survival.

  tcga gse40419 gse31210 gene bulk microarray univariate

• 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

• Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

  PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups

  Has reproduction · 49

  ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC

  ptc degs key bulk kegg weighted

• Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.

  PMID 41744654 · PMC12938635 · Biology · 2026 · 7 claims · 7 setups

  Has reproduction · 100

  A meta-analysis of eight microarray studies (10 sub-studies) produced a combined list of 4218 statistically significant DEGs between AD and healthy brain at an adjP cut-off of 0.001

  post-mortem combined sub-studies down-regulated microarray differential statistical

• QTLs for heat-induced stomatal anatomy underpin gas exchange variation in field-grown wheat.

  PMID 42231893 · PMC13223016 · Frontiers in plant science · 2026 · 8 claims · 6 setups

  Has reproduction · 100

  Heat stress via delayed sowing reduces stomatal conductance (gs) and gas exchange efficiency (gse) despite unchanged theoretical maximum anatomical conductance (gsmax), revealing a decoupling of structural potential and physiological performance under stress.

  field-grown microscope wheat field stomatal in-field deep

• Identification and Mechanisms of Osteocyte Subsets Involved in the Pathological Progression of Osteoporosis.

  PMID 41250977 · PMC12850396 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Has reproduction · 57

  Single-cell sequencing of mouse femurs identifies six distinct osteocyte subsets (C1-C6) after excluding contaminating erythroid clusters

  femoral osteocyte dmp1-cre+ bhr-ocys single-cell monocle flow

• Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing.

  PMID 30208848 · PMC6134632 · BMC genomics · 2018 · 8 claims · 7 setups

  Has reproduction · 50

  2867 circRNAs were identified in soybean flower buds via high-throughput sequencing with RNase R enrichment, of which 1009 were differentially expressed between NJCMS1A and NJCMS1B

  flower roots analysis parental high-throughput quantitative pcr

• Evaluating native-like structures of RNA-protein complexes through the deep learning method.

  PMID 36828844 · PMC9958188 · Nature communications · 2023 · 8 claims · 7 setups

  Has reproduction · 67

  DRPScore identifies native-like RNA-protein structures with higher success rates than ITScore-PR, DARS-RNP, and 3dRPC across bound and unbound testing sets.

  bound-bound unbound-bound unbound-unbound bacillus structure interface secondary

• Autoantibody profiling for the study and treatment of autoimmune disease.

  PMID 12223102 · PMC128938 · Arthritis research · 2002 · 8 claims · 8 setups

  Full-text index only

  Custom-fabricated antigen microarrays (spotted on poly-L-lysine-coated glass slides) enable multiplex profiling of autoantibody responses in autoimmune disease sera.

  serum antigen-antibody antigens fetal spotted elisa microarray

• The post-genomic era for a select few.

  PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

  Full-text index only

  The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

  takifugu physcomitrella coli vibrio comparative genetic dna-microarray

• Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

  PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

  Full-text index only

  GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

  chromosome genomic comparative phylohmmcons conserved

• Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

  PMID 17158152 · PMC1802574 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  GLR is a novel maximum-likelihood measure of gene loss rate that probabilistically weighs all possible ancestral phyletic patterns rather than relying on a single parsimonious reconstruction.

  synthetic eukaryotic simulated 16-species analytical comparative simulation

• Pathway analysis of kidney cancer using proteomics and metabolic profiling.

  PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups

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  31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue

  ccrcc rcc computational random gel immunoblotting immunohistochemistry

• NovelFam3000--uncharacterized human protein domains conserved across model organisms.

  PMID 16533400 · PMC1440326 · BMC genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  NovelFam3000 is an online data centre unifying bioinformatics resource links, news, comments, and user-submitted experimental data (including a Gene Characterization Index) for ~3000 uncharacterized Pfam-B/DUF domain families conserved across worm, fly, and human

  lines mammalian hek drosophila rt-pcr immunofluorescence counterstaining

• hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

  PMID 17207965 · PMC4647941 · Genomics · 2007 · 8 claims · 7 setups

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  hORFeome v3.1 is a resource of 12,212 cloned human ORFs representing 10,214 genes, a 51% expansion over hORFeome v1.1

  mgc cloned orfs genome gateway orf blat

• Metabolism as a complex genetic trait, a systems biology approach: implications for inborn errors of metabolism and clinical diseases.

  PMID 18836848 · PMC4319114 · Journal of inherited metabolic disease · 2008 · 7 claims · 8 setups

  Full-text index only

  Synergistic heterozygosity — cumulative heterozygous mutations at multiple loci in functionally related metabolic pathways — can cause physiologically relevant reduction of pathway flux and disease.

  models liver sucrose vlcad-deficient physiological blue sucrose

• The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

  PMID 19940846 · PMC2923224 · Clinical pharmacology and therapeutics · 2010 · 8 claims · 8 setups

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  PMT identified sequence variants in 129 membrane transporter genes in the SLC and ABC superfamilies, discovering over 3100 SNPs

  sophie mammalian xenopus lymphoblastoid resequencing cellular heterologous

• Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

  PMID 35949126 · PMC9682560 · Anatolian journal of cardiology · 2022 · 7 claims · 7 setups

  Full-text index only

  10 key genes (TCF7L2, CACNA1C, NRP1, GABBR2, FANCC, DCK, CCDC88C, TCF12, ABLIM1, PBX1) are regulated by both aberrant DNA methylation and miRNA activity in atherosclerosis

  aorta cardiovascular peripheral blood methylation mirna expression

• Discovery and hypothesis generation through bioinformatics.

  PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups

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  Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data

  genome chemokine gene-expression proteins genome-wide phylogenetic microarray