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).

• Characterization of 954 bovine full-CDS cDNA sequences.

  PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

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  954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

  bovine translated bflic sequence est primer-walking blastp

• A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

  PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups

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  Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families

  pad phylogenetic est est-based

• Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

  PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

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  89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

  normalized rainbow salmonids microsatellite sanger pcr

• 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

• 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

• Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

  PMID 17442112 · PMC1863428 · BMC cancer · 2007 · 7 claims · 5 setups

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  CYYR1 mRNA undergoes a 'subtle' alternative splicing event generating two isoforms (CAG- and CAG+) differing by a single alanine codon at the exon3/exon4 junction

  neuroendocrine tumors normal cyyr1 rt-pcr quantitative psti

• Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

  PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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  A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

  refseq tp53 tumor 154-gene est paired array

• TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates.

  PMID 17986453 · PMC2238949 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  TranspoGene catalogs TEs within protein-coding genes of seven species (human, mouse, chicken, zebrafish, fruit fly, nematode, sea squirt), classified as proximal promoter, exonized, exonic, or intronic TEs.

  chicken normal tes genes genomic exon microrna

• 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

• Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

  PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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  XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

  hct116 macaque cos-7 genomic cdna est molecular

• Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

  PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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  Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

  liver genomic tissues embryos rt-pcr genomic secondary