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).

• Independent component analysis reveals new and biologically significant structures in micro array data.

  PMID 16762055 · PMC1557674 · BMC bioinformatics · 2006 · 7 claims · 8 setups

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  ICA applied to three microarray datasets reveals many biologically significant components, including low-ranking ones not obvious by rank alone

  acute serum-stimulated head aml microarray clust term

• Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.

  PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups

  Has reproduction · 71

  Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.

  breast colorectal brca representative gene comparative multi-omic

• T1DBase, a community web-based resource for type 1 diabetes research.

  PMID 15608258 · PMC540049 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  T1DBase is an integrated, open-access web resource that unifies genetic, genomic, and biological data to support type 1 diabetes (T1D) research

  pancreatic t1d tissues nod microarray genetic est-based

• Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

  PMID 15601541 · PMC3525069 · Human genomics · 2004 · 8 claims · 6 setups

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  DNA microarray gene expression profiling generates robust molecular classifications for many tumour types (brain, breast, colon, gastric, kidney, leukaemia, lymphoma, lung, melanoma, ovary, prostate, etc.)

  breast sars serum tumour microarray custom mass

• BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression.

  PMID 18497862 · PMC2375115 · PLoS genetics · 2008 · 8 claims · 6 setups

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  BRCA1 and BRCA2 pathogenic mutation carriers have similar post-irradiation LCL gene expression profiles to each other, more so than to BRCAX samples without an LCS variant

  lymphoblastoid lcl gene microarray unsupervised t-test

• Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

  PMID 18212748 · PMC2243141 · British journal of cancer · 2008 · 5 claims · 6 setups

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  LC-MS/MS proteomic analysis of stage I lung adenocarcinoma specimens identified myosin IIA and vimentin as candidate biomarker proteins with signal intensities that differed significantly among patient outcome groups

  surgically tryptic set lysates lc-ms mascot immunohistochemistry

• Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

  PMID 18204449 · PMC2684619 · Nature genetics · 2008 · 8 claims · 8 setups

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  Mutations in GLE1, an mRNA export mediator, cause LCCS1

  lccs1 laahd finnish healthy genomic microsatellite carrier

• A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

  PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups

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  A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD

  cases patients postmortem whole-genome cox linear

• The molecular characterization and clinical management of multiple myeloma in the post-genome era.

  PMID 19657360 · PMC3686133 · Leukemia · 2009 · 8 claims · 8 setups

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  GEP identifies distinct molecular subgroups of MM associated with differing clinical features and survival outcomes

  myeloma cd138-immunomagnetically plasma bone-marrow filter-based gene-expression targeted

• Brain progranulin expression in GRN-associated frontotemporal lobar degeneration.

  PMID 19649643 · PMC3104467 · Acta neuropathologica · 2010 · 8 claims · 8 setups

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  GRN transcript haploinsufficiency, previously shown in blood-derived cells, does not hold in most brain regions of GRN mutation carriers

  peripheral postmortem hek293 qrt-pcr microarray rt-pcr

• Genomics--from Neanderthals to high-throughput sequencing.

  PMID 16934106 · PMC1779599 · Genome biology · 2006 · 8 claims · 8 setups

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  Next-generation sequencing platforms (GS20/454 and Solexa) can deliver the throughput and cost reductions needed for population-scale and medical resequencing.

  bacterial ion-channel drosophila arrays next-generation pooled multiplex

• Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.

  PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups

  Has reproduction · 89

  Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM

  european cis-pqtl myocardial geo mendelian bayesian differential

• DESE: estimating driver tissues by selective expression of genes associated with complex diseases or traits.

  PMID 31694669 · PMC6836538 · Genome biology · 2019 · 8 claims · 8 setups

  Has reproduction · 56

  DESE is a unified iterative framework that estimates driver tissues of complex diseases/traits from tissue-selective expression of GWAS-associated genes, and outputs prioritized susceptibility genes as a byproduct

  tissues schizophrenia bipolar coronary rna-seq gwas gene

• Bone marrow ectopic expression of a non-coding RNA in childhood T-cell acute lymphoblastic leukemia with a novel t(2;11)(q11.2;p15.1) translocation.

  PMID 18947387 · PMC2579299 · Molecular cancer · 2008 · 8 claims · 8 setups

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  A novel t(2;11)(q11.2;p15.1) translocation was identified as the sole cytogenetic abnormality in a childhood T-ALL case

  bone genomic da926692 g-banding fish vectorette

• Calibrating the performance of SNP arrays for whole-genome association studies.

  PMID 18584036 · PMC2432039 · PLoS genetics · 2008 · 8 claims · 7 setups

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  Previous SNP array genetic coverage estimates are inflated due to SNP overfitting and sample overfitting, since they were evaluated on the same HapMap SNPs/individuals used to design the arrays.

  american liver simulated hapmap snp gene simulation-based

• A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

  PMID 18547137 · PMC2504036 · PLoS medicine · 2008 · 7 claims · 8 setups

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  GEM models combined with in-depth proteomic analysis provide a useful strategy to identify candidate cancer markers applicable to human disease with potential for early detection

  plasma immunodepleted pancreatic shotgun two-dimensional immunodepletion

• Genetic and functional association of FAM5C with myocardial infarction.

  PMID 18430236 · PMC2383879 · BMC medical genetics · 2008 · 8 claims · 5 setups

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  SNPs within FAM5C show genetic linkage to and association with myocardial infarction in the GENECARD family-based sample

  genecard cathgen donor aortic genome-wide case-control expression

• Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.

  PMID 33086062 · PMC7649750 · Cell reports · 2020 · 8 claims · 8 setups

  Has reproduction · 59

  KMT2D is a potent tumor suppressor in melanoma

  hmel-brafv600e tyr-creert2 tma kmt2d pooled xenograft genetically

• More breast cancer genes?

  PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

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  A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

  tumours five independent ataxia-telangiectasia comparative haplotype linkage

• PRKCA and multiple sclerosis: association in two independent populations.

  PMID 16596167 · PMC1420678 · PLoS genetics · 2006 · 8 claims · 8 setups

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  PRKCA (protein kinase C alpha) on 17q24 is associated with MS in Finnish families

  finnish canadian unrelated blood snp dense multipoint