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).
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A simple and robust method for connecting small-molecule drugs using gene-expression signatures.
PMID 18518950 · PMC2464610 · BMC bioinformatics · 2008 · 8 claims · 4 setups
A new method for building reference gene-expression profiles and scoring/testing connections improves on the original Connectivity Map by enabling statistical significance testing of connections.
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BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.
PMID 19919682 · PMC3091323 · Genome biology · 2009 · 8 claims · 4 setups
BioGPS aggregates distributed, third-party gene annotation resources into a single customizable portal for human, mouse, and rat genes.
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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
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.
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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
FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data
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Tissue compartment analysis for biomarker discovery by gene expression profiling.
PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups
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
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Has reproduction · 60
Core transcriptional signatures of phase change in the migratory locust.
PMID 31292921 · PMC6881432 · Protein & cell · 2019 · 8 claims · 7 setups
PhaseCore genes defined by AC-PCA contribution to phase differentiation predict phase status with >87.5% accuracy
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Has reproduction · 80
Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.
PMID 40680064 · PMC12322963 · Journal of proteome research · 2025 · 8 claims · 7 setups
928 differentially accumulating mRNAs (564 up, 364 down) were identified between exponential and stationary phase
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Has reproduction · 78
4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.
PMID 33301041 · PMC7708080 · Nucleic acids research · 2020 · 7 claims · 8 setups
A 4mC orphan MTase (lomA) is present only in the pathogenic (P) clade of Leptospira and methylates CTAG motifs.
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Has reproduction · 73
Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.
PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups
N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort
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GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.
PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups
GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes
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High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.
PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups
The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.
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Gene expression and isoform variation analysis using Affymetrix Exon Arrays.
PMID 18990248 · PMC2585104 · BMC genomics · 2008 · 8 claims · 7 setups
The Exon Array performs comparably to 3'-targeted platforms (Illumina, U133) at the gene expression level, though interplatform correlation is slightly lower than between the two 3' platforms.
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3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.
PMID 19917133 · PMC2781828 · BMC genomics · 2009 · 8 claims · 4 setups
3' tag DGE transcript profiles are highly reproducible between technical and biological replicates, across libraries made at different labs, and across two generations of Illumina Genome Analyzers (GA I and GA II).
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Recent additions and improvements to the Onto-Tools.
PMID 15980579 · PMC1160233 · Nucleic acids research · 2005 · 7 claims · 3 setups
The Onto-Tools back-end database was redesigned around the Entrez Gene data model after NCBI phased out LocusLink in February 2005.
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Has reproduction · 86
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.
PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups
RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.
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Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.
PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups
A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning
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MitoP2: the mitochondrial proteome database--now including mouse data.
PMID 16381964 · PMC1347489 · Nucleic acids research · 2006 · 8 claims · 8 setups
MitoP2 is a database integrating manually annotated mitochondrial reference proteins, functions, and disease associations for yeast, human, and mouse, with cross-species orthologue mapping
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Has reproduction · 51
Polyploidy and the petal transcriptome of Gossypium.
PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups
Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.
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GeneTrail--advanced gene set enrichment analysis.
PMID 17526521 · PMC1933132 · Nucleic acids research · 2007 · 8 claims · 2 setups
GeneTrail is a comprehensive, easy-to-use web-based tool for gene set enrichment analysis supporting both Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA)
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Has reproduction · 37
A Bayesian approach to accurate and robust signature detection on LINCS L1000 data.
PMID 32003771 · PMC7203754 · Bioinformatics (Oxford, England) · 2020 · 6 claims · 4 setups
A novel Bayesian-based peak deconvolution algorithm gives unbiased likelihood estimations for peak locations and characterizes peaks with probability-based z-scores.