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 15

System / cell line: refseq ✕ Assay: motif ✕ Clear

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
ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

PMID 17984078 · PMC2238997 · Nucleic acids research · 2008 · 6 claims · 4 setups

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ARED Organism and ARED-Integrated are new/updated public databases cataloguing ARE-containing mRNAs/genes in human, mouse and rat

6x6 ortholog 3'utr comparative chi-squared
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

putative nonredundant homo genes computational pssm semantic
Comprehensive splice-site analysis using comparative genomics.

PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups

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Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.

refseq u2-type genes comparative information phylogenetic
Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

muscle-specific bovine refseq cardiac novo est blastn
Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

PMID 18187510 · PMC2275096 · Nucleic acids research · 2008 · 8 claims · 6 setups

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G-richness downstream of the TSS is strand-biased, concentrated on the nontemplate strand, with a peak at +200 to +300 bp

refseq chicken random genome-wide quadparser regulatory
Computational analysis of splicing errors and mutations in human transcripts.

PMID 18194514 · PMC2234086 · BMC genomics · 2008 · 8 claims · 4 setups

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Retained introns are significantly shorter than constitutively spliced introns

refseq genes intron exon computational splice prediction
Computational comparison of two mouse draft genomes and the human golden path.

PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups

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The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)

newly genome chromosome genomic blat blastn repeat
Comparative genomics of Drosophila and human core promoters.

PMID 16827941 · PMC1779564 · Genome biology · 2006 · 8 claims · 6 setups

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Drosophila core promoters contain 298 highly significant (p≤1e-16) non-randomly positioned 8-mers within 100 bp of the TSS, grouped into 15 distinct DNA motifs

drosophila core genome-wide mono gene
The distribution of SNPs in human gene regulatory regions.

PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

gene mammalian promoter experimentally genome-wide computational binding
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

PMID 18684996 · PMC2532738 · Nucleic acids research · 2008 · 8 claims · 7 setups

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SISSRs identifies binding sites from ChIP-Seq short reads with much higher resolution than the standard region-clustering approach

cd4+ jurkat hela computational chip-seq novo motif
CEAS: cis-regulatory element annotation system.

PMID 16845068 · PMC1538818 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CEAS is the first web server to streamline genome-scale ChIP-chip downstream analyses for biologists without strong bioinformatics support

genome genomic chip-chip repeat-masked conservation
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

genome poly est cdna est blast cdna
Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

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The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis

Experiments

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

ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

Comprehensive splice-site analysis using comparative genomics.

Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

Computational analysis of splicing errors and mutations in human transcripts.

Computational comparison of two mouse draft genomes and the human golden path.

Comparative genomics of Drosophila and human core promoters.

The distribution of SNPs in human gene regulatory regions.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

CEAS: cis-regulatory element annotation system.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.