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).

• Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

  PMID 17447839 · PMC1853124 · PLoS computational biology · 2007 · 8 claims · 8 setups

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  A new algorithm using spliced ESTs (cross-validated against Known Genes and GenBank mRNA) comprehensively maps bidirectional promoters in the human genome

  genome transcripts tissues proteins comparative taf250 cpg

• Bioinformatics Analysis of the Characteristics and Correlation of m6A Methylation in Breast Cancer Progression.

  PMID 35655723 · PMC9148239 · Contrast media & molecular imaging · 2022 · 8 claims · 8 setups

  Has reproduction · 48

  Breast cancer samples can be classified into 4 m6A subtypes (quiescent, m6A methylation, protein-binding, mixed) based on Z-score median of Set1 (writer+reader) and Set2 (eraser) gene expression

  breast tcga-brca gse25066 bioinformatics survival alternative

• ECgene: an alternative splicing database update.

  PMID 17132829 · PMC1716719 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  ECgene provides functional annotation (domain, GO, expression pattern) for alternatively spliced genes

  nine genome sage cdna genome-based chi-squared sage

• Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

  PMID 18545673 · PMC2409220 · PloS one · 2008 · 8 claims · 6 setups

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  An integrative ad-hoc functional GO analysis combining threshold-based (Fisher exact/hypergeometric) and threshold-free (Kolmogorov-Smirnov) statistics, plus term-to-parent comparisons, detects disease-relevant splicing events from exon array data.

  mg-thymoma colon exon fluorescent reverse

• From microarrays to genome duplications.

  PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

  tumor cancer plated saccharomyces comparative nonsense-mediated cell-based

• The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

  PMID 17108355 · PMC1669709 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  ASAP II expands human alternative splicing data ~3-fold over the previous ASAP database, to ~89,078 distinct alternative splicing relationships in 11,717 genes

  genome animal aligned est genome-wide comparative est