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).

• Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE).

  PMID 15339345 · PMC517707 · BMC bioinformatics · 2004 · 7 claims · 5 setups

  Full-text index only

  A Bayesian mixture model is proposed to account for within-class biological variability in SAGE/Digital-Northern/MPSS tag counting data.

  astrocytoma same sage classical beta-binomial

• Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

  PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups

  Full-text index only

  Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions

  normal genome-wide same omim microarray sage computational

• The UCSC Genome Browser Database: 2008 update.

  PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.

  zebrafish yale vertebrate non-human sage expression snp

• Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

  PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups

  Full-text index only

  Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia

  cervical independent computational long real-time gene

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

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

  Full-text index only

  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

• Tissue compartment analysis for biomarker discovery by gene expression profiling.

  PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups

  Full-text index only

  TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures

  kidney pure serial rt-pcr sage histo-morphometry

• FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

  PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

  user-supplied gene predicted interactome gene kegg transcription

• Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

  PMID 19906709 · PMC2811022 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  A genome-wide catalog of up to ~9000 overlapping antisense loci (23,782 non-redundant SAT pairs, clustered into 8894) was compiled and stored in the USAGP database

  genome affymetrix antisense mirna computational microarray sage

• Gene function in the mammalian genome, courtesy of the mouse.

  PMID 12537544 · PMC151280 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Mosaicism of Mus musculus domesticus and Mus musculus musculus haplotypes exists across the inbred laboratory mouse genome, and genome-wide haplotype mapping can enhance positional cloning

  inbred genome mice model genome-wide large-scale phenotypic