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).

• Onto-Tools: new additions and improvements in 2006.

  PMID 17584796 · PMC1933142 · Nucleic acids research · 2007 · 8 claims · 3 setups

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  OE2GO enables functional profiling for organisms lacking public-domain annotations by allowing users to supply custom GO-format annotation files and OBO-format ontology files

  specified pathway functional example

• miRGator: an integrated system for functional annotation of microRNAs.

  PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

  genome predicted tissues organs computational functional mirna

• Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

  PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

  user-supplied ranked gene fasta-formatted functional gene novo

• TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.

  PMID 34197621 · PMC8464036 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 60

  TRAPID 2.0 is a web application performing global characterization of de novo transcriptomes via structural, functional, and taxonomic annotation in an initial processing phase, followed by an exploratory phase of downstream analyses.

  mmetsp query putative ciliate taxonomic similarity non-coding

• Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

  PMID 25018105 · PMC4377509 · Cell · 2014 · 8 claims · 7 setups

  Has reproduction · 64

  L1 starvation induces changes in endogenous 22G small RNAs (STGs) that are inherited for at least three generations in fed descendants.

  elegans small small sequencing lifespan

• Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells.

  PMID 14709176 · PMC395736 · Genome biology · 2003 · 8 claims · 5 setups

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  Distinct cellular processes are coregulated by androgen while others are essentially unaffected in LNCaP cells

  lncap computational icat western hypergeometric

• Pseudofam: the pseudogene families database.

  PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments

  eukaryotic over pseudogenes pseudogene blast family sequence

• Human synthetic lethal inference as potential anti-cancer target gene detection.

  PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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  Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

  saccharomyces sapiens ihsln genes database phylogenetic gene

• 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

• Towards precise classification of cancers based on robust gene functional expression profiles.

  PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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  Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

  nci60 lymphoma fep go-annotated cdna recursive hypergeometric

• Bias of selection on human copy-number variants.

  PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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  Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

  genome human-mouse cnv-encompassed inbred comparative randomization molecular

• Reconstruction of human protein interolog network using evolutionary conserved network.

  PMID 17493278 · PMC1885812 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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  A relative conservation score derived from maximal quasi-cliques in protein interaction networks, combined with other interaction features, can score and rank predicted human interologs for confidence.

  ppi sequences interaction predicted interolog orthology quasi-clique

• Distribution and effects of nonsense polymorphisms in human genes.

  PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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  Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

  genome genes nonsense snps genome-wide snp codon

• Transcriptome analysis reveals differential splicing events in IPF lung tissue.

  PMID 24647608 · PMC3960165 · PloS one · 2014 · 8 claims · 6 setups

  Has reproduction · 81

  873 genes are differentially expressed in IPF lung tissue versus healthy controls at FDR<5%, with more up-regulated than down-regulated genes.

  lung discovery gene gse24206 sequencing rna-seq real-time

• 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

  Has reproduction · 27

  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.

  radish assembled rna-seq novo functional

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

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

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  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