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 8

System / cell line: pwm ✕ Assay: expression ✕ Clear

Adaptively inferring human transcriptional subnetworks.

PMID 16760900 · PMC1681499 · Molecular systems biology · 2006 · 8 claims · 7 setups

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A multivariate linear spline (MARS-based) model correlating PWM binding scores with log expression ratios can identify active cis-motif combinations in mammalian promoters without requiring gene clustering.

liver proximal hela predicted microarray computational novo
In silico discovery of transcription regulatory elements in Plasmodium falciparum.

PMID 18257930 · PMC2268928 · BMC genomics · 2008 · 7 claims · 8 setups

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GEMS, using hypergeometric scoring and PWM parameter optimization, reliably identifies high-confidence cis-regulatory elements in the AT-rich, repeat-rich P. falciparum genome

falciparum plasmodium invasion invasion-related microarray motif comparative
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
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups

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A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle

genome candidate gxd medline evolutionary gene expression
Identification of functional SNPs in the 5-prime flanking sequences of human genes.

PMID 15717931 · PMC550646 · BMC genomics · 2005 · 6 claims · 5 setups

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7 of 10 candidate SNPs tested by EMSA showed reproducible allele-specific differences in TF-DNA complex binding/stability

flanking synthetic genomic cloned comparative electrophoretic rflp
CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

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CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

cd4+ hela imr90 embryonic chip-seq computational gene
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

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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

human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence
Severe combined immunodeficiency (SCID) and attention deficit hyperactivity disorder (ADHD) associated with a Coronin-1A mutation and a chromosome 16p11.2 deletion.

PMID 19097825 · PMC2692687 · Clinical immunology (Orlando, Fla.) · 2009 · 8 claims · 7 setups

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CORO1A deficiency, caused by a paternal 2bp frameshift mutation combined with a maternal de novo 600kb deletion at chromosome 16p11.2, is the molecular cause of this patient's T-B+NK+ SCID

ebv-transformed genomic father peripheral intracellular snp sequencing

Experiments

Adaptively inferring human transcriptional subnetworks.

In silico discovery of transcription regulatory elements in Plasmodium falciparum.

Comprehensive splice-site analysis using comparative genomics.

Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

Identification of functional SNPs in the 5-prime flanking sequences of human genes.

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

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.

Severe combined immunodeficiency (SCID) and attention deficit hyperactivity disorder (ADHD) associated with a Coronin-1A mutation and a chromosome 16p11.2 deletion.