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).

• Intronic alternative splicing regulators identified by comparative genomics in nematodes.

  PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

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  Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

  elegans database transgenic comparative est cross-species

• The loss of transcriptional inhibition by the photoreceptor-cell specific nuclear receptor (NR2E3) is not a necessary cause of enhanced S-cone syndrome.

  PMID 17438525 · PMC2669504 · Molecular vision · 2007 · 8 claims · 8 setups

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  NR2E3 LBD fused to a heterologous Gal4 DBD mediates dose-dependent transcriptional repression on Gal4-responsive reporters.

  cos-1 hela luciferase western electrophoretic

• Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

  PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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  MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

  engineered p53 computational yeast-based regional homology

• Discovery of genes activated by the mitochondrial unfolded protein response (mtUPR) and cognate promoter elements.

  PMID 17849004 · PMC1964532 · PloS one · 2007 · 8 claims · 5 setups

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  mtUPR responsive genes (YME1L1, MPPβ, Tim17A, NDUFB2, Endonuclease G, Thioredoxin 2, plus previously known ClpP, Cpn60/10, MtDnaJ) all contain a CHOP element in their promoters

  genome cos-7 promoters bioinformatic promoter-luciferase site-directed

• Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity.

  PMID 16061936 · PMC1182164 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Oct-1, Oct-2, PU.1, Sp1 and Sp3 interact in vitro with the pol gene HS7 region

  nuclear spodoptera hiv-infected nih3t3 electrophoretic supershift emsa

• A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

  PMID 19890225 · PMC6177227 · Pharmacogenetics and genomics · 2009 · 7 claims · 6 setups

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  Extensive sequencing of UGT1A4 (promoter to exon 1+2000bp) identified numerous novel polymorphisms: 13 intronic, 39 promoter, and 14 exonic variants (10 causing amino acid changes)

  genomic hek293 hepg2 microsomes pcr site-directed luciferase

• No direct effect of the -521 C/T polymorphism in the human dopamine D4 receptor gene promoter on transcriptional activity.

  PMID 16723017 · PMC1481588 · BMC molecular biology · 2006 · 8 claims · 3 setups

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  The -521 C/T SNP has no significant effect on transcriptional activity of the DRD4 promoter in any of three neural cell lines tested

  sk-n-f1 rt-pcr luciferase

• A novel missense mutation in DAX-1 with an unusual presentation of X-linked adrenal hypoplasia congenita.

  PMID 17308433 · PMC3479083 · Hormone research · 2007 · 7 claims · 6 setups

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  A novel C794G transversion causing missense mutation T265R in DAX1 (NR0B1) is responsible for X-linked adrenal hypoplasia congenita in this kindred

  genomic tsa201 unspecified proband sequence modified full-length

• 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

• Biased exon/intron distribution of cryptic and de novo 3' splice sites.

  PMID 16141195 · PMC1197134 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  Cryptic 3'ss (from 3'YAG consensus mutations) are significantly more frequent in exons than in introns

  disease authentic hek293t nuclear literature shapiro-senapathy splicing

• Investigations on a clinically and functionally unusual and novel germline p53 mutation.

  PMID 12085209 · PMC2746598 · British journal of cancer · 2002 · 8 claims · 7 setups

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  A novel germline 7 base pair insertion in exon 5 of p53 (causing frameshift from codon 161 with a stop at codon 182) was identified in a patient with osteosarcoma at age 22 and choroid plexus papilloma at age 29.

  peripheral yeast saos-2 genomic fasay apoptotic

• Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.

  PMID 19859740 · PMC2939908 · Human genetics · 2010 · 7 claims · 7 setups

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  NOS2 promoter haplotypes are not consistently associated with malaria severity or malarial anemia across three independent Tanzanian study populations

  tanzanian a549 muheza-tanga sscp pcr restriction