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).

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining

• Towards alignment independent quantitative assessment of homology detection.

  PMID 17205117 · PMC1762415 · PloS one · 2006 · 8 claims · 6 setups

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  The Fhom Estimator uses the prevalence of a conserved protein feature (X) in two protein sets to estimate the fraction of true homologs among paired proteins, independent of alignment quality.

  curated homologene swiss-prot fruit signalp homologene-based fhom

• Diversity of tRNA genes in eukaryotes.

  PMID 17088292 · PMC1693877 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  The number of tRNA genes having the same anticodon but different sequences elsewhere (isodecoder genes) varies significantly (10–246) across 11 eukaryotes despite isoacceptor numbers being similar (41–55)

  eukaryotic bacterial genome synthetic genome-wide sequence manual

• Ensembl 2006.

  PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.

  cow ensembl snps genome gene whole-genome pairwise

• miRGen: a database for the study of animal microRNA genomic organization and function.

  PMID 17108354 · PMC1669779 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  miRGen is an integrated database combining Genomics, Targets, and Clusters interfaces to study miRNA genomic organization and function across 11 animal genomes

  animal genome mouse-human mirna genomic mirna cross-species

• Gene-disease relationship discovery based on model-driven data integration and database view definition.

  PMID 19042916 · PMC2639000 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 4 setups

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  Explicit gene–disease relationships can be formulated as candidate gene definitions (e.g., co-localization, dysregulation, functional similarity) that may include intermediary orthologous or interacting genes

  acgr disease term-based database case

• oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

  PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups

  Has reproduction · 49

  oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.

  hg19 large-scale gene-based jaspar tfbs sequence-based anchored

• Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes.

  PMID 18828897 · PMC2760871 · Genome biology · 2008 · 8 claims · 8 setups

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  The overlap between phosphoproteomes of six eukaryotes (human, mouse, fly, yeast, plant, zebrafish) is significantly greater than expected by chance.

  liver fruit yeast plant high-throughput comparative

• Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

  PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species

  est gene worm fly blat-based transcription comparative

• A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

  PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

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  Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

  genes hela proteins worm co-expression quantitative functional

• 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

• The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

  PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

  est clustered sequences sequence est sequence orf

• COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.

  PMID 36350658 · PMC9825429 · Nucleic acids research · 2023 · 8 claims · 6 setups

  Has reproduction · 84

  COXPRESdb version 8 adds CoexMap (UMAP-based genome-scale coexpression visualization), KEGG pathway enrichment summaries, and CoexPub (literature-linking tool) as new analysis features.

  animal same coexpression gene rnaseq-based microarray-based pathway

• Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

  PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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  Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

  species genomic jmjd6 jmjc reciprocal comparative est

• Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

  PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

  Has reproduction · 83

  Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

  species microrna atlas microarray rna-seq microrna