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).

Publications 1.3k Datasets 392.5k Experiments 16

System / cell line: unigene ✕ Assay: functional ✕ Clear

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

embryonic high-quality unique m15e est sequence comparative
Recent additions and improvements to the Onto-Tools.

PMID 15980579 · PMC1160233 · Nucleic acids research · 2005 · 7 claims · 3 setups

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The Onto-Tools back-end database was redesigned around the Entrez Gene data model after NCBI phased out LocusLink in February 2005.

homo example mus functional pathway cross-database
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
Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

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MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical
Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

PMID 16195578 · PMC1240112 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Alternative splices in 10,818 human-mouse gene pairs can be classified as conserved, novel, or diverged based on genomic and transcript-level cross-species comparison.

orthologous diverse tissues gene comparative est microarray
ECgene: genome annotation for alternative splicing.

PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

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ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

brca2 rgs17 organs cdna genomic genome transcript
Inferring combinatorial regulation of transcription in silico.

PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

upstream monocytes same tfbs microarray permutation
De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.

PMID 29451882 · PMC5815590 · PloS one · 2018 · 7 claims · 7 setups

Has reproduction · 45

This is the first de novo transcriptomic analysis of Cornus officinalis, providing fundamental gene and biosynthetic pathway information.

cornus frozen high-quality officinalis bulk extraction novo
Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.

PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups

Has reproduction · 73

De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp

suaeda rna-seq novo blastx
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.

PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups

Has reproduction · 46

De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases

sparassis latifolia bulk transcriptome sequence
A DNA microarray survey of gene expression in normal human tissues.

PMID 15774023 · PMC1088941 · Genome biology · 2005 · 6 claims · 6 setups

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Unsupervised hierarchical clustering of gene expression groups normal tissue samples largely according to anatomic location, cellular composition, or physiologic function.

normal common computational each two-color comparative unsupervised
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
ARED 3.0: the large and diverse AU-rich transcriptome.

PMID 16381826 · PMC1347415 · Nucleic acids research · 2006 · 7 claims · 6 setups

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ARED 3.0 computationally mapped more than 4000 ARE-mRNAs to the human genome, representing 5-8% of human genes.

records est est-derived combined computational est sequence
Identification and characterization of insect-specific proteins by genome data analysis.

PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

drosophila insect-core locusta insect-specific comparative est functional
MODBASE: a database of annotated comparative protein structure models and associated resources.

PMID 16381869 · PMC1347422 · Nucleic acids research · 2006 · 8 claims · 7 setups

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MODBASE is a database of automatically calculated comparative protein structure models covering all UniProt sequences matchable to a known structure

uniprot non-redundant complexes saccharomyces comparative pairwise domain-domain
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

Has reproduction · 70

AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr

Experiments

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

Recent additions and improvements to the Onto-Tools.

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

Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

ECgene: genome annotation for alternative splicing.

Inferring combinatorial regulation of transcription in silico.

De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.

Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.

De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.

A DNA microarray survey of gene expression in normal human tissues.

Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

ARED 3.0: the large and diverse AU-rich transcriptome.

Identification and characterization of insect-specific proteins by genome data analysis.

MODBASE: a database of annotated comparative protein structure models and associated resources.

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).