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 19

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

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
Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

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Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

caninum ceylanicum est bioinformatic functional
Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

embryonic high-quality unique m15e est sequence comparative
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

lncap lncap-derived r1881-treated massively blast blat
Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

chinese tissues skeletal pk15 full-length real-time gfp
Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.

PMID 16204447 · PMC1243803 · Nucleic acids research · 2005 · 8 claims · 3 setups

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A Bayesian model incorporating experimental covariates (array, pen, probe, dye, scanning) can estimate absolute transcript concentrations from spotted microarray intensities without needing calibration of each sample or gene individually

cervix same spotted quantitative
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
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
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
Characterization of the Schistosoma transcriptome opens up the world of helminth genomics.

PMID 14709167 · PMC395727 · Genome biology · 2003 · 8 claims · 5 setups

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Near-complete transcriptome complements have now been described for S. japonicum and S. mansoni

japonicum mansoni est blastx functional
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
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

Has reproduction · 27

A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

radish assembled rna-seq novo functional
Application of functional genomics to primate endometrium: insights into biological processes.

PMID 17118168 · PMC1775064 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 7 setups

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Gene expression profiles differ distinctly across proliferative, early-, mid-, and late-secretory phases of the human menstrual cycle, reflecting sequential estradiol and progesterone action.

endometrial uterus whole-genome cdna oligonucleotide
Database resources of the National Center for Biotechnology Information.

PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

genbank genomic eukaryotic completely sequence rapid est
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
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
Comparative genomics comes of age.

PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

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Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

orthologous chromosome chimpanzee somatic-cell comparative targeted tiled
More biology from the sequence.

PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups

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The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.

schizosaccharomyces chromosome genome cervical whole-genome sequence genome

Experiments

The gene guessing game.

Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.

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

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

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.

Characterization of the Schistosoma transcriptome opens up the world of helminth genomics.

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

Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

Application of functional genomics to primate endometrium: insights into biological processes.

Database resources of the National Center for Biotechnology Information.

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.

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

Comparative genomics comes of age.

More biology from the sequence.