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).

• With the finished human genome in hand, what next?

  PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

  domestic saccharomyces systemic schistosoma comparative functional genetic

• Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans.

  PMID 22119442 · PMC3250924 · Cell · 2011 · 8 claims · 8 setups

  Has reproduction · 68

  viRNA-mediated silencing of the FR1gfp Flock House virus is transmitted to RNAi-deficient (rde-1 or rde-4 homozygous) progeny and persists for many ensuing generations, i.e. an acquired antiviral trait is inherited.

  transgenic elegans four gfp genetic template-independence

• Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in acute myeloid leukemia.

  PMID 19835597 · PMC2770485 · Molecular cancer · 2009 · 8 claims · 8 setups

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  MLL-mutant (MLL mu) AML cell lines show significantly lower TSG promoter methylation than MLL wild-type (MLL wt) AML cell lines

  acute mll lines bone ms-mlpa hhai methylation-specific

• PDGFRA defines the mesenchymal stem cell Kaposi's sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment.

  PMID 31881074 · PMC6980685 · PLoS pathogens · 2019 · 8 claims · 8 setups

  Has reproduction · 85

  PDGFRA(+)/SCA-1(+) bone marrow-derived MSCs (Pα(+)S MSCs) are KS spindle-cell progenitors

  bone kshv-infected k-pα nude flow kshv immunofluorescence

• The integrated world of functional genomics.

  PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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  Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

  cerevisiae sequenced elegans drosophila chromatin integration comparative

• Reactivation of a developmentally silenced embryonic globin gene.

  PMID 34290235 · PMC8295333 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  In embryonic (primitive) erythroid cells, the ζ-gene lies within a ~65 kb sub-TAD of open, acetylated chromatin and physically interacts with the α-globin super-enhancer.

  primitive embryos ζ-venus atac-seq dnasei chip-seq

• Inactivation of O6-methylguanine-DNA methyltransferase by promoter CpG island hypermethylation in gastric cancers.

  PMID 12085181 · PMC2375420 · British journal of cancer · 2002 · 6 claims · 8 setups

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  Loss of MGMT expression in gastric carcinomas frequently results from promoter CpG island hypermethylation.

  gastric consecutive snu-620 methylation-specific immunohistochemistry western

• Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

  PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups

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  DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases

  cd19+ leukemia raji jurkat quantitative cobra chromatin

• A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

  PMID 28642491 · PMC5481429 · Scientific reports · 2017 · 6 claims · 8 setups

  Has reproduction · 76

  Hnf4a is a major transcriptional regulator of Dnajc22.

  mus tissues liver-specific kidney bulk microarray chip-seq

• SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells.

  PMID 32770939 · PMC7430845 · BMC genomics · 2020 · 8 claims · 5 setups

  Has reproduction · 94

  SOX10 binds preferentially at proximal promoter elements directly over TSSs in Schwann cells in vivo, identifying candidate SOX10-regulated promoters.

  sciatic schwann differentiating tn5prime chip-seq gene

• TP73 allelic expression in human brain and allele frequencies in Alzheimer's disease.

  PMID 15175114 · PMC420466 · BMC medical genetics · 2004 · 8 claims · 6 setups

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  A -386G/A SNP in the TP73 P3 promoter is weakly but significantly associated with AD risk in a tri-ethnic elderly population.

  brain peripheral sk-nsh-n genomic rt-pcr direct snp

• The genetics of regulatory variation in the human genome.

  PMID 16004727 · PMC3525257 · Human genomics · 2005 · 8 claims · 7 setups

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  Naturally-occurring gene expression variation among individuals is common across species (yeast, Drosophila, mouse, fish, maize, primates, humans) and has a significant genetic component.

  ceph immortalised lymphoblastoid individuals reporter allelic microarray

• Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

  PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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  Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

  muscle-specific bovine refseq cardiac novo est blastn

• Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

  PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups

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  Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes

  5'-flanking upstream transiently genomic comparative tfbs promoter-reporter

• Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

  PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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  A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

  myeloid reference selected genome-localized microarray promoter k-medoids

• Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

  PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

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  A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

  gene upstream chimpanzee reconstructed minimum sequence ancestral

• Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

  PMID 18003658 · PMC2248751 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  p110 CUX1 is recruited to promoters of cell cycle-related target genes preferentially during S phase

  hela hs578t nih3t3 genomic chap-chip conventional scanning

• CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

  PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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  CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

  neuroblastoma nlf athymic methylation-specific quantitative soft

• 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

• Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

  PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups

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  Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS

  peripheral blood pooled trio gene quantitative promoter