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 35

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

PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

PMID 17202160 · PMC1899096 · Nucleic acids research · 2007 · 7 claims · 5 setups

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PolyA_DB 2 catalogs poly(A) sites for genes in human, mouse, rat, chicken and zebrafish, identified by aligning cDNA/ESTs with genome sequences

sequences poly cdna trace pssm-based
CRSD: a comprehensive web server for composite regulatory signature discovery.

PMID 16845073 · PMC1538777 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CRSD is a comprehensive web server integrating six large-scale databases (UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway, GO) plus two newly constructed genome-wide databases (MRS and TRS) for composite regulatory signature discovery

gene 3'-utr promoter user-submitted genome-wide microrna binding
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

PMID 16845044 · PMC1538898 · Nucleic acids research · 2006 · 8 claims · 2 setups

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The ASPIC algorithm, using an optimization procedure that minimizes splice site predictions and transcript isoforms from multiple EST-genome alignments, outperforms other similar AS-prediction tools in sensitivity and selectivity

hnrpr specified comparative algorithm
Alternative polyadenylation of cyclooxygenase-2.

PMID 15872218 · PMC1088970 · Nucleic acids research · 2005 · 8 claims · 5 setups

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The human COX-2 gene undergoes alternative polyadenylation using proximal and distal polyadenylation signals

cox-2 ht29 hela bioinformatics western rnase
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
Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.

PMID 17038195 · PMC1618849 · BMC genomics · 2006 · 8 claims · 6 setups

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EXPOLDB is a novel database integrating human gene expression variability data (including monozygotic twin comparisons) with (TG/CA)n repeat polymorphism information

blood genomic genes housekeeping microarray repeat est-based
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

maqc hepatocytes japanese illeum microarray dasl sequence
T1DBase, a community web-based resource for type 1 diabetes research.

PMID 15608258 · PMC540049 · Nucleic acids research · 2005 · 8 claims · 6 setups

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T1DBase is an integrated, open-access web resource that unifies genetic, genomic, and biological data to support type 1 diabetes (T1D) research

pancreatic t1d tissues nod microarray genetic est-based
Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

PMID 16204454 · PMC1243798 · Nucleic acids research · 2005 · 8 claims · 4 setups

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Cis-encoded natural antisense RNAs show striking preferential complementarity to 3′-UTRs of their target genes in human and mouse genomes

human-mouse model genome-wide comparative computational
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
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
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

unigene shuffled real genomes genome-wide alignment gene
POCUS: mining genomic sequence annotation to predict disease genes.

PMID 14611661 · PMC329128 · Genome biology · 2003 · 8 claims · 6 setups

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Genes predisposing to the same disease tend to share functional annotation IDs (GO/InterPro) more than expected by chance

omim genome disease comparative pocus expression-id
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
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.

PMID 16925843 · PMC1810558 · Genome biology · 2006 · 8 claims · 4 setups

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Adding model states for specific biological features (signal peptides, CpG islands, etc.) to non-comparative GHMM gene finders did little or nothing to enhance predictive accuracy, sometimes reducing it.

encode genes invertebrate initio comparative training
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
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

genome chimpanzee sult1a3 est blast-like comparative pairwise
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
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
Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

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DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

extremely families genome sanger case-control family-based

Experiments

PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

CRSD: a comprehensive web server for composite regulatory signature discovery.

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

Alternative polyadenylation of cyclooxygenase-2.

ECgene: genome annotation for alternative splicing.

Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

T1DBase, a community web-based resource for type 1 diabetes research.

Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

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

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

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

POCUS: mining genomic sequence annotation to predict disease genes.

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

JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.

Recent additions and improvements to the Onto-Tools.

Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

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

Inferring combinatorial regulation of transcription in silico.

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.