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: genome-wide ✕ Clear

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
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

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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
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
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
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
Design and analysis issues in genome-wide somatic mutation studies of cancer.

PMID 18692126 · PMC2820387 · Genomics · 2009 · 6 claims · 4 setups

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Two-stage (discovery + validation) sequencing designs efficiently allocate resources and can produce highly informative candidate driver gene lists even with relatively small sample sizes.

hypothetical panel colorectal germline simulation targeted genome-wide
Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.

PMID 12702206 · PMC154576 · Genome biology · 2003 · 8 claims · 6 setups

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Segmental duplications comprise 3.53% (107.4/3,043.1 Mb) of the June 2002 human genome assembly

genome refseq-annotated chromosome chromosome-wide e-pcr ambsnp
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
Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

hgmd refseq aligned svm svm reciprocal inter-species
Geographical genomics of human leukocyte gene expression variation in southern Morocco.

PMID 19966804 · PMC2798927 · Nature genetics · 2010 · 8 claims · 8 setups

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Gene expression differs substantially between locations (up to 38% of transcripts), driven largely by a rural-versus-urban lifestyle contrast rather than ethnicity or gender.

peripheral blood genotype randomly genome-wide population admixture
The UCSC Genome Browser Database: 2008 update.

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

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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
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
Ensembl 2008.

PMID 18000006 · PMC2238821 · Nucleic acids research · 2008 · 8 claims · 6 setups

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The Ensembl regulatory build integrates multiple genome-wide functional genomics datasets to automatically annotate regulatory regions and assign putative functions across the genome.

embryonic amniota multi-species individuals automated chip-chip comparative
In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

PMID 17726045 · PMC2094079 · Nucleic acids research · 2007 · 8 claims · 6 setups

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Two exonic mutations, PINK1 E417G and PARK7 E64D, disrupt binding to U1 snRNA and cause skipping of the mutation-harboring exon

hek293 genome lymphocytes minigene artificial genome-wide
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

The distribution of SNPs in human gene regulatory regions.

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

Comparative genomics of Drosophila and human core promoters.

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

CEAS: cis-regulatory element annotation system.

Design and analysis issues in genome-wide somatic mutation studies of cancer.

Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.

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

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

Geographical genomics of human leukocyte gene expression variation in southern Morocco.

The UCSC Genome Browser Database: 2008 update.

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

Ensembl 2008.

In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

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.