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).

• Gene Expression Analysis Platform (GEAP): A highly customizable, fast, versatile and ready-to-use microarray analysis platform.

  PMID 34927664 · PMC8754388 · Genetics and molecular biology · 2021 · 8 claims · 2 setups

  Has reproduction · 83

  GEAP is a GUI-based microarray analysis platform combining a C# front-end with an R (RTerm) back-end via the rgeap package, enabling analysis independent of manufacturer/platform.

  sqlite microarray software microarray

• Seeded Bayesian Networks: constructing genetic networks from microarray data.

  PMID 18601736 · PMC2474592 · BMC systems biology · 2008 · 8 claims · 4 setups

  Full-text index only

  Seeding Bayesian Network analysis with prior networks derived from literature and/or PPI data improves recovery of known gene-gene interactions compared to BN analysis without a seed

  leukemia interactome pubmed-indexed computational microarray yeast literature

• Systems biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

  Full-text index only

  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

  PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

  Full-text index only

  Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

  saliva amplified extracted differentially genome quality extraction

• Overview of microarray analysis of gene expression and its applications to cervical cancer investigation.

  PMID 18182341 · PMC7129792 · Taiwanese journal of obstetrics & gynecology · 2007 · 6 claims · 5 setups

  Full-text index only

  Oligonucleotide microarray and cDNA microarray are the two main microarray platforms used to study gene expression genome-wide.

  cervical cdna microarray combinatorial

• Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies.

  PMID 34107850 · PMC8806433 · Bioengineered · 2021 · 6 claims · 6 setups

  Has reproduction · 55

  TYR, TYRP1, DCT and LARP7 are biomarkers associated with vitiligo

  vitiligo merged robust gse90880 gene robust kegg

• Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.

  PMID 32365491 · PMC7281456 · Cancers · 2020 · 8 claims · 7 setups

  Has reproduction · 35

  ZBTB38 expression is decreased in localised prostate cancer and further decreased in metastatic prostate cancer compared to non-cancerous prostate tissue

  prostate localised gene rna-sequencing clinico-pathological

• A distinct epigenetic signature at targets of a leukemia protein.

  PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups

  Full-text index only

  Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve

  32d sequence gene bioinformatic real-time

• Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

  PMID 18772890 · PMC2671642 · Nature · 2008 · 8 claims · 5 setups

  Full-text index only

  NF1 is a genuine human glioblastoma suppressor gene, inactivated by mutation, deletion, or expression loss in at least 23% of GBM samples

  glioblastoma gbm matched sequenced copy gene methylation

• An integrative genomic and epigenomic approach for the study of transcriptional regulation.

  PMID 18365023 · PMC2266992 · PloS one · 2008 · 8 claims · 7 setups

  Full-text index only

  Integrative analysis combining gene expression, DNA methylation, and H3K9 acetylation data reveals hundreds of additional differentially expressed genes missed by gene expression arrays alone

  aml computational help chip-chip gene

• CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

  PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups

  Full-text index only

  Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.

  breast commercial vertebrate genes cdna activity computational

• Managing incidental findings in human subjects research: analysis and recommendations.

  PMID 18547191 · PMC2575242 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 5 setups

  Full-text index only

  Little guidance currently exists on managing research IFs, and no consensus exists on the best approach across genetic/genomic and imaging research domains.

  affected large research consent linkage genomic structural

• Functional genomics of early cortex patterning.

  PMID 16515721 · PMC1431711 · Genome biology · 2006 · 7 claims · 6 setups

  Full-text index only

  The neocortical protomap is established as continuous rostro-caudal gradients of gene expression in progenitor cells, not discrete compartments

  neocortex embryonic fgfr1-mutant cortex oligonucleotide situ microarray

• Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.

  PMID 19943934 · PMC2794290 · BMC cancer · 2009 · 8 claims · 5 setups

  Full-text index only

  Hundreds of genes differentiate GISTs according to KIT versus PDGFRA mutation and expression status, despite no discriminative profile for clinical/pathological parameters.

  frozen genomic formalin-fixed differentially microarray sequencing quantitative

• Have microarrays failed to deliver for developmental biology?

  PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups

  Full-text index only

  Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.

  drosophila caenorhabditis developing xenopus cdna genome-wide microarray

• A big circuit model.

  PMID 12940284 · PMC1316925 · Environmental health perspectives · 2003 · 8 claims · 8 setups

  Full-text index only

  In early prostate carcinogenesis, apoptosis signals are primarily suppressed rather than growth rate being increased.

  prostate blood model genes microarray proteomic gene

• Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

  PMID 15804357 · PMC1129089 · BMC genomics · 2005 · 8 claims · 6 setups

  Full-text index only

  MagT1 is a novel mammalian Mg2+ transporter with channel-like properties, showing no amino acid sequence identity to other known transporters

  kidney mdct tissues xenopus oligonucleotide northern real-time

• Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.

  PMID 16846522 · PMC1543642 · BMC genomics · 2006 · 7 claims · 6 setups

  Full-text index only

  PPT frequency is significantly elevated in yeast meiotic recombination hot spots compared with cold spots

  cerevisiae genome chimpanzee hot computational microarray comparative

• Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

  PMID 17000641 · PMC1636412 · Nucleic acids research · 2006 · 8 claims · 6 setups

  Full-text index only

  An anonymous SHyP oligonucleotide microarray can capture genomic signatures of DNA sequence variation from any organism, including a previously unsequenced species

  genomic gonystylus subset restriction-digested custom self-self blast

• The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.

  PMID 17145711 · PMC1751528 · Nucleic acids research · 2007 · 7 claims · 5 setups

  Full-text index only

  GermOnline is a cross-species systems browser providing comprehensive curated information on genes and gene products relevant for sexual reproduction across nine model organisms including human.

  saccharomyces mus rodent classical tiling comparative