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).

• Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

  PMID 19848416 · PMC2789179 · Journal of proteome research · 2009 · 6 claims · 6 setups

  Full-text index only

  Transgelin (TAGLN), transgelin-2 (TAGLN2), and cyclophilin A (PPIA) are overexpressed in lung adenocarcinoma tissue compared to matched normal lung

  matched excised additional formalin-fixed 2-d lc-ms quantitative

• KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

  PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

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  KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

  diffuse-type liver renal anaplastic differential proteomic proteomics

• Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

  PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort

  breast paired embryonic hesc-derived bulk rt-qpcr immunofluorescence

• L2L: a simple tool for discovering the hidden significance in microarray expression data.

  PMID 16168088 · PMC1242216 · Genome biology · 2005 · 8 claims · 4 setups

  Full-text index only

  L2L systematically compares a user's differentially expressed gene list against a database of published differentially expressed gene lists to find statistically significant overlaps and generate hypotheses about shared mechanisms

  mammalian user-supplied diabetic uniprot compiled l2l re-analysis

• 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

• Differential protein expression in human corneal endothelial cells cultured from young and older donors.

  PMID 18852868 · PMC2565687 · Molecular vision · 2008 · 8 claims · 5 setups

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  Cultured HCEC protein profiles show age-related differences between young and older donors

  corneal 2-d trypsin-digested confluent 2-d gel maldi-tof

• Mutation and deletion analysis of GFR alpha-1, encoding the co-receptor for the GDNF/RET complex, in human brain tumours.

  PMID 10408842 · PMC2362327 · British journal of cancer · 1999 · 8 claims · 3 setups

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  No mutations were found in the coding region of GDNF in any of the 36 brain tumours analysed

  sporadic tumour tumour-derived pcr loss semi-quantitative

• DNA demethylation is associated with malignant progression of lower-grade gliomas.

  PMID 30760837 · PMC6374451 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction

  Nearly half of IDH-mutant glioblastomas that progressed from lower-grade gliomas show characteristic partial DNA demethylation in previously methylated (G-CIMP) genomic regions of their initial tumor.

  gliomas neural analysis tcga methylation whole-exome sequencing

• Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles.

  PMID 37444556 · PMC10340377 · Cancers · 2023 · 7 claims · 4 setups

  Has reproduction · 90

  Different EV isolation methods vary in reproducibility for isolating small RNAs and have characteristic effects on small RNA composition, with differential ultracentrifugation showing the highest variability/lowest replicability.

  evs plasma small isolation validation

• To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.

  PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups

  Has reproduction · 33

  C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory

  coronary scrna-seq five type single-cell doublet copy

• Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.

  PMID 17299390 · PMC2360060 · British journal of cancer · 2007 · 8 claims · 6 setups

  Full-text index only

  DDR1 is significantly upregulated in NSCLC tumour tissue compared with matched normal lung tissue

  nsclc matched lung quantitative pcr genomic

• Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

  PMID 18772397 · PMC2848990 · Science (New York, N.Y.) · 2008 · 8 claims · 6 setups

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  Pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations

  pancreatic computational targeted prevalence snp

• Proteomics in animal models of Alzheimer's and Parkinson's diseases.

  PMID 18703168 · PMC2630427 · Ageing research reviews · 2009 · 8 claims · 6 setups

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  Proteomics studies in APPSw transgenic mice reveal differential expression of proteins involved in metabolism, ubiquitin/proteasome system, cellular transport, synaptic/axonal integrity, and inflammation

  app swedish p301l gskβ page proteomics redox

• The use of neuroproteomics in drug abuse research.

  PMID 19926406 · PMC3947580 · Drug and alcohol dependence · 2010 · 8 claims · 8 setups

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  Neuroproteomic technologies (2D-DIGE, iTRAQ, ICAT, etc.) enable identification of protein-level changes underlying effects of drugs of abuse such as amphetamine, morphine, cocaine, and alcohol.

  rodent brain postmortem sectioned 2d-dige itraq heat

• Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

  PMID 15626334 · PMC5172349 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 5 setups

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  Well-resolved, reproducible 2-DE profiles of human lung squamous carcinoma and normal bronchial epithelial tissues were obtained under optimized conditions (0.75-mg protein load, TCA precipitation)

  lung scanned excised peptide 2-d 2-de maldi-tof-ms

• Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids.

  PMID 29983891 · PMC6033374 · Oncotarget · 2018 · 8 claims · 6 setups

  Has reproduction · 65

  UC patient-derived epithelial organoids histologically phenocopy primary UC tissue, while non-IBD organoids resemble healthy colonic epithelium.

  patient-derived h3k27ac histology immunohistochemistry bulk

• Genomic and proteomic profiling II: comparative assessment of gene expression profiles in leiomyomas, keloids, and surgically-induced scars.

  PMID 17718906 · PMC2039739 · Reproductive biology and endocrinology : RB&E · 2007 · 7 claims · 4 setups

  Full-text index only

  1124 transcripts (1103 genes; 732 over-expressed, 371 under-expressed) are differentially expressed in leiomyomas compared to keloids/incisional scars

  keloid leiomyoma microarray quantitative

• Methods for genome-wide analysis of DNA methylation in intestinal tumors.

  PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups

  Full-text index only

  Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.

  cd19+ lung gpx1 tumor mira medip goldengate

• Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

  PMID 24304889 · PMC3964963 · Nucleic acids research · 2014 · 8 claims · 6 setups

  Has reproduction · 84

  Expression Atlas is a value-added database providing gene, protein and splice variant expression across cell types, organism parts, developmental stages, diseases and other biological/experimental conditions, built from manually curated high-quality microarray and RNA-sequencing experiments from ArrayExpress.

  organisms arrayexpress-derived pride rna-sequencing single-channel two-colour

• iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

  PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

  nsclc coad brca tcga scrna-seq bulk rna-seq