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).

• Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

  PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups

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  Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.

  pools individual same parental pooled individual test-retest

• IRSN-23 gene diagnosis enhances breast cancer subtype classification and predicts response to neoadjuvant chemotherapy: new validation analyses.

  PMID 40128415 · PMC11993443 · Breast cancer (Tokyo, Japan) · 2025 · 8 claims · 8 setups

  Has reproduction · 71

  IRSN-23 Gp-R patients have significantly higher pCR rates than Gp-NR patients without anti-HER2 therapy, across the OUH cohort and multiple independent public datasets

  breast microarray rna-seq exome

• Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling.

  PMID 18157127 · PMC2397541 · Nature genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Homozygous truncating mutations in PCNT cause Seckel syndrome

  consanguineous genomic lymphoblastoid lcls snp-microarray sanger immunofluorescence

• Silhouette scores for assessment of SNP genotype clusters.

  PMID 15760469 · PMC555759 · BMC genomics · 2005 · 7 claims · 5 setups

  Full-text index only

  Silhouette scores provide a relevant, objective numeric measure of SNP genotype cluster quality, condensing tightness and separation into a single value from -1.0 to 1.0.

  genomic blood extended hybridized single genomic multiplex

• CLEAN: CLustering Enrichment ANalysis.

  PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

  Full-text index only

  The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

  four breast combined hierarchical cluster csimm-based

• TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.

  PMID 33705981 · PMC9403021 · Genomics, proteomics & bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 79

  TSUNAMI is a freely accessible web-based tool suite that mines gene co-expression network (GCN) modules from public (GEO, TCGA) or user-uploaded numerical omics data and performs downstream gene set enrichment analysis.

  gse17537 36th first gene circos survival

• Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

  PMID 17888167 · PMC2082044 · BMC genomics · 2007 · 8 claims · 6 setups

  Full-text index only

  A proposed coupled two-way clustering (CTWC/SPC) method combined with a GO-based functional concept consistency score can identify compact, robust gene subsets that define clinically meaningful DLBCL subtypes

  dlbcl identified microarray oligonucleotide coupled

• First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_.

  PMID 30691411 · PMC6348648 · BMC bioinformatics · 2019 · 8 claims · 2 setups

  Has reproduction · 30

  COMMAND>_ is a flexible multi-user web-application that allows users to search and download gene expression experiments, extract relevant information from experiment files, re-annotate microarray platforms, and present data in a coherent data model.

  small microarray microarray probe-to-gene

• Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.

  PMID 32365491 · PMC7281456 · Cancers · 2020 · 8 claims · 8 setups

  Has reproduction · 35

  ZBTB38 mRNA expression is significantly lower in prostate cancer than in normal/benign prostate tissue, and further reduced in metastatic versus localised tumours

  localised tcga taylor metastatic microarray rna-sequencing clinico-pathological

• Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.

  PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 71

  Mitophagy-related genes associated with immune infiltration have diagnostic/prognostic significance in ALS

  blood als microarray spearman univariate

• Reverse Engineering of the Pediatric Sepsis Regulatory Network and Identification of Master Regulators.

  PMID 34680414 · PMC8533457 · Biomedicines · 2021 · 7 claims · 8 setups

  Has reproduction · 67

  A set of 15 TFs was identified as sepsis-specific master regulators of pediatric sepsis, dividing into two non-overlapping clusters.

  blood cd4+ pbmc regulons microarray differential master

• Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

  PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

  Full-text index only

  A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

  myeloid reference selected genome-localized microarray promoter k-medoids

• In silico discovery of transcription regulatory elements in Plasmodium falciparum.

  PMID 18257930 · PMC2268928 · BMC genomics · 2008 · 7 claims · 8 setups

  Full-text index only

  GEMS, using hypergeometric scoring and PWM parameter optimization, reliably identifies high-confidence cis-regulatory elements in the AT-rich, repeat-rich P. falciparum genome

  falciparum plasmodium invasion invasion-related microarray motif comparative

• Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

  PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups

  Full-text index only

  Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.

  liver saccharomyces mdeg independent microarray transcription chromosomal

• Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

  PMID 26538066 · PMC4634735 · BMC medical genomics · 2015 · 8 claims · 7 setups

  Has reproduction · 83

  A multigene expression biomarker from PBMCs accurately classifies familial breast cancer (FBC) status

  pbmcs utah blood normal microarray svm-rfe svm

• CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.

  PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 4 setups

  Has reproduction · 87

  CoINcIDE is a novel framework for discovering patient subtypes across multiple datasets that requires no between-dataset transformations (e.g., batch correction)

  breast ovarian simulated gene consensus simulated

• Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.

  PMID 34143800 · PMC8213194 · PloS one · 2021 · 8 claims · 7 setups

  Has reproduction · 75

  306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified from three independent GEO microarray datasets comparing EOC and adjacent normal ovarian tissue

  eoc analysis overlapping pubmed microarray kegg protein-protein

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

  PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 8 claims · 5 setups

  Has reproduction · 62

  A DNN model built on 34 top-ranked hub genes achieves the highest prediction accuracy (AUC 92.11%) for distinguishing primary from bone-metastasized tumors

  breast degs geo tcga microarray protein-protein machine

• Identification of a novel 10 immune-related genes signature as a prognostic biomarker panel for gastric cancer.

  PMID 34382341 · PMC8446556 · Cancer medicine · 2021 · 8 claims · 8 setups

  Has reproduction

  A 10-IRG prognostic signature (BMPR1B, GHR, IL11RA, INHBB, NPR3, OBP2A, PTN, R3HDML, TAC1, TPM2) predicts overall survival in gastric cancer.

  gastric tcga-stad overlapping candidate microarray gene rna-seq

• Effect of PAIP1 on the metastatic potential and prognostic significance in oral squamous cell carcinoma.

  PMID 35153296 · PMC8841500 · International journal of oral science · 2022 · 8 claims · 8 setups

  Has reproduction · 10

  PAIP1 mRNA and protein levels are increased in OSCC/HNSCC tissues and cell lines compared to normal tissue/cells

  hnscc tcga cptac oscc microarray rna-seq quantitative