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 9

System / cell line: transcription ✕ Assay: exon-intron ✕ Clear

Designating eukaryotic orthology via processed transcription units.

PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs

ortholog blat exon-intron blast-based
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
Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups

Has reproduction · 75

A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.

mcf7 promoter gene signals pol-ii clustering transcription
Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

bac heart ccs genomic genomic rt-pcr transcription
CEAS: cis-regulatory element annotation system.

PMID 16845068 · PMC1538818 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CEAS is the first web server to streamline genome-scale ChIP-chip downstream analyses for biologists without strong bioinformatics support

genome genomic chip-chip repeat-masked conservation
Mutation analysis of the MSMB gene in familial prostate cancer.

PMID 19997100 · PMC2816656 · British journal of cancer · 2010 · 8 claims · 5 setups

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No deleterious mutations were found in the MSMB coding region in 192 familial prostate cancer cases

germline blood 161-nt genotype sanger taqman transcription
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

Has reproduction · 100

44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

tetramorium bicarinatum vpg venom whole-genome blast gene
Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

vertebrate cdna pedf complete genomic rt-pcr phylogenetic
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

Experiments

Designating eukaryotic orthology via processed transcription units.

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

Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

CEAS: cis-regulatory element annotation system.

Mutation analysis of the MSMB gene in familial prostate cancer.

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

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