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 18

System / cell line: ests ✕ Assay: prediction ✕ Clear

Using ESTs to improve the accuracy of de novo gene prediction.

PMID 16817966 · PMC1534067 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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TWINSCAN_EST combines EST alignments with TWINSCAN via a trainable 'ESTseq' representation and improves exact gene structure prediction accuracy on the whole C. elegans genome

elegans genome chromosome novo gene partial
Integrating alternative splicing detection into gene prediction.

PMID 15705189 · PMC550657 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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An integrative intrinsic/extrinsic method was implemented in the gene finder EuGÈNE (as EuGÈNE-M) to detect AS evidence from aligned transcripts and generate alternative optimal gene predictions consistent with each detected AS event.

arabidopsis araset thaliana transcript-to-genome initio comparative
The truth about mouse, human, worms and yeast.

PMID 15601543 · PMC3525071 · Human genomics · 2004 · 8 claims · 8 setups

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Comparing genomes in pairs or larger sets (mouse-human, C. elegans-C. briggsae, multiple Saccharomyces, human-pufferfish, etc.) reveals unsuspected genes and helps eliminate false-positive gene predictions

mouse-human homo tetraodon region comparative est cross-species
Non-EST based prediction of exon skipping and intron retention events using Pfam information.

PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

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A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

refseq dbest genome pfam initio est comparative
GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

PMID 15608261 · PMC540076 · Nucleic acids research · 2005 · 8 claims · 7 setups

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GeneTide integrates UniGene, DoTS, AceView, BLAT/GeneLoc genomic alignment, and GeneAnnot probe-set data into a unified Consensus/Uniqueness/Score scheme to associate ESTs with GeneCards genes

transcriptome genome spliced transcripts est genomic splice-orientation
A novel de novo PAX6 mutation in an Ashkenazi-Jewish family with aniridia.

PMID 18334930 · PMC2255027 · Molecular vision · 2008 · 7 claims · 5 setups

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A novel heterozygous de novo PAX6 frameshift mutation (c.577_578insG, insG@Gly72) in exon 6 causes autosomal dominant aniridia with congenital cataract, nystagmus, and glaucoma in this family.

genomic pax6 direct microsatellite blast
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
The gene guessing game.

PMID 11025532 · PMC2448377 · Yeast (Chichester, England) · 2000 · 8 claims · 6 setups

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Published methods for estimating human gene number diverge widely, from ~30,000 to over 140,000 genes.

genomic ests tetraodon genome cpg est comparative
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
Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

PMID 16925839 · PMC1810554 · Genome biology · 2006 · 7 claims · 5 setups

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Pairagon+N-SCAN_EST, using only native alignments, was as accurate as ENSEMBL and ExoGean in the EGASP mRNA/EST evidence assessment

encode genome cdna-to-genome novo comparative
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

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3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

bovine cow coding blast-based ensembl gene
Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.

PMID 19880432 · PMC2780955 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 8 claims · 5 setups

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Identified 23,241 human genes transcribed into protein-coding mRNAs using full-length cDNA and 5'-EST sequence data

tissues genome full-length genes full-length genome orf
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

est clustered sequences sequence est sequence orf
Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

PMID 16855283 · PMC1524921 · Nucleic acids research · 2006 · 8 claims · 5 setups

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Four novel brain-specific paternally expressed transcripts (BB077283, BM117114, AK080843, AV328498) were identified and validated on proximal Chr 7.

tissues inter-subspecies placenta genomic microarray rt-pcr sequencing
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
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

PMID 17201911 · PMC1774567 · BMC genomics · 2007 · 8 claims · 5 setups

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A computational EST-based pipeline can identify UTR-SNPs that are statistically over-represented in cancerous versus normal tissue libraries

est acute 100-nt whole-genome est-based pcr-based secondary
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
Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

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GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr

Experiments

Using ESTs to improve the accuracy of de novo gene prediction.

Integrating alternative splicing detection into gene prediction.

The truth about mouse, human, worms and yeast.

Non-EST based prediction of exon skipping and intron retention events using Pfam information.

GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

A novel de novo PAX6 mutation in an Ashkenazi-Jewish family with aniridia.

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

The gene guessing game.

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

Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

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.

In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

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

Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.