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 30

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

Introduction of in vitro transcribed ENO1 mRNA into neuroblastoma cells induces cell death.

PMID 16359544 · PMC1327688 · BMC cancer · 2005 · 8 claims · 6 setups

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ENO1 has tumour suppressor activity

sk-n-as neuroblastoma genomic growth tunel real-time
Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.

PMID 18500686 · PMC2516917 · The Prostate · 2008 · 8 claims · 5 setups

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Identified 32 genes (38 cDNAs) with an expression pattern of highest levels in seminal vesicle, lower in normal prostate, and lowest in prostate cancer

normal prostate microarray cdna cross-tissue gene
Finding disease candidate genes by liquid association.

PMID 17915034 · PMC2246280 · Genome biology · 2007 · 7 claims · 6 setups

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LA can detect functionally associated genes that are not directly co-expressed by identifying a mediating gene Z whose expression level changes the correlation between X and Y.

nci_cdna gnf_2002 finnish gnf_2004 liquid transmission correlation
Predicting candidate genes for human deafness disorders: a bioinformatics approach.

PMID 16854223 · PMC1564145 · BMC genomics · 2006 · 8 claims · 4 setups

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A bioinformatic approach combining expression databases and protein interaction data narrows ~2400 candidate genes across deafness loci to a manageable set of candidates.

genomic developing proteins positional expression protein-protein
Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups

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A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval

cdna image hbs1l ahi1 rt-pcr est northern
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
Towards precise classification of cancers based on robust gene functional expression profiles.

PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

nci60 lymphoma fep go-annotated cdna recursive hypergeometric
Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.

PMID 15115540 · PMC420239 · BMC genomics · 2004 · 6 claims · 3 setups

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Bioinformatic sequence comparison of 60,770 RIKEN FANTOM2 mouse cDNA clones identified 2,578 sequences with 70-85% identity to known human disease genes/proteins

riken medline sequence manual semi-automated
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

PMID 15534692 · PMC526178 · PLoS biology · 2004 · 8 claims · 6 setups

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Intramolecular pairs of oppositely oriented Alu elements within the same pre-mRNA form dsRNA foldback structures that are major substrates for A-to-I RNA editing

huge brain pre-mrna greater genomic rt-pcr quantitative
A computational study of off-target effects of RNA interference.

PMID 15800213 · PMC1072799 · Nucleic acids research · 2005 · 8 claims · 5 setups

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The chance of RNAi off-target effects is considerable, ranging from 5% to 80% depending on organism and parameters, when using exact sequence identity between siRNA and transcripts.

schizosaccharomyces caenorhabditis homo pombe off-target mismatch-tolerant rational
A novel GJA8 mutation causing a recessive triangular cataract.

PMID 18483562 · PMC2375854 · Molecular vision · 2008 · 8 claims · 6 setups

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A homozygous single base-pair insertion (c.776insG) in GJA8 causes a recessive triangular nuclear cataract in two affected siblings.

proband's blood-derived genomic family rt-pcr pcr restriction
Computational analysis of splicing errors and mutations in human transcripts.

PMID 18194514 · PMC2234086 · BMC genomics · 2008 · 8 claims · 4 setups

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Retained introns are significantly shorter than constitutively spliced introns

refseq genes intron exon computational splice prediction
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

genome transcriptome gene genes full-length genome cdna
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

Has reproduction · 57

ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

arabidopsis pacbio randomly illumina pacbio nanopore
Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups

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Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.

orthologues nih-3t3 3t3 mefs bioinformatic egfp co-transfection
Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

PMID 18507500 · PMC2429944 · PLoS medicine · 2008 · 7 claims · 7 setups

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At least 36 of the 189 newly mutated CAN genes are targets of promoter CpG island hypermethylation, often in both colon and breast cancer cell lines

breast same selected hct116 expression methylation-specific rt-pcr
Comparative analysis of cancer genes in the human and chimpanzee genomes.

PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

chimpanzee non-human cancer comparative pcr targeted
A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

PMID 18301748 · PMC2244703 · PloS one · 2008 · 8 claims · 7 setups

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FOXO1a mRNA and protein expression are elevated in human liver compared to chimpanzee liver

chimpanzee hepg2 promoters liver quantitative western sirna
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
Endotoxin-tolerant mice have mutations in Toll-like receptor 4 (Tlr4).

PMID 9989976 · PMC2192941 · The Journal of experimental medicine · 1999 · 8 claims · 8 setups

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The Lps locus was fine-mapped to a 0.9-cM interval spanning a 1.7-Mb genomic contig on mouse chromosome 4.

c3h genomic bac multiple-tissue genetic yac direct

Experiments

Introduction of in vitro transcribed ENO1 mRNA into neuroblastoma cells induces cell death.

Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.

Finding disease candidate genes by liquid association.

Predicting candidate genes for human deafness disorders: a bioinformatics approach.

Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

Characterization of 954 bovine full-CDS cDNA sequences.

Towards precise classification of cancers based on robust gene functional expression profiles.

Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.

Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

A computational study of off-target effects of RNA interference.

A novel GJA8 mutation causing a recessive triangular cataract.

Computational analysis of splicing errors and mutations in human transcripts.

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

Comparative analysis of cancer genes in the human and chimpanzee genomes.

A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

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

Endotoxin-tolerant mice have mutations in Toll-like receptor 4 (Tlr4).