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).
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Glycomic approach for potential biomarkers on prostate cancer: profiling of N-linked glycans in human sera and pRNS cell lines.
PMID 19126968 · PMC3827814 · Disease markers · 2008 · 8 claims · 5 setups
Glycomic profiling of N-linked glycans in serum can reveal potential biomarkers distinguishing prostate cancer patients from controls
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Fingerprinting cancer development.
PMID 14694892 · PMC1241638 · Environmental health perspectives · 2003 · 8 claims · 6 setups
Protein microarrays can detect phosphoprotein fingerprints that identify early-stage cancer or monitor drug toxicity.
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Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.
PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups
MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue
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A taxonomy of epithelial human cancer and their metastases.
PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups
Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters
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Has reproduction · 76
Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.
PMID 26286638 · PMC4541321 · Scientific reports · 2015 · 6 claims · 4 setups
DRW-GM integrates gene expression and metabolomic profiles via directed random walk on a global gene–metabolite pathway graph to weight genes by topological importance and infer reproducible pathway activities
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A big circuit model.
PMID 12940284 · PMC1316925 · Environmental health perspectives · 2003 · 8 claims · 8 setups
In early prostate carcinogenesis, apoptosis signals are primarily suppressed rather than growth rate being increased.
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Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.
PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups
Current syndromic disease classification lacks specificity despite historically serving clinicians well
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Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.
PMID 18500686 · PMC2516917 · The Prostate · 2008 · 8 claims · 5 setups
Identified 32 genes (38 cDNAs) with an expression pattern of highest levels in seminal vesicle, lower in normal prostate, and lowest in prostate cancer
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Identification of gene interactions associated with disease from gene expression data using synergy networks.
PMID 18234101 · PMC2258206 · BMC systems biology · 2008 · 8 claims · 4 setups
Synergy of a gene pair with respect to disease, defined as I(G1,G2;C) - [I(G1;C)+I(G2;C)], identifies gene pairs that interact cooperatively with respect to a phenotype rather than independently.
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[Research progress in SELDI-TOF MS and its clinical applications].
PMID 17168305 · PMC7148935 · Sheng wu gong cheng xue bao = Chinese journal of biotechnology · 2006 · 4 claims · 4 setups
Proteinchip profiling based on SELDI-TOF MS is a powerful and innovative proteomic technology for biomarker discovery and diagnostic/prognostic assay development.
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Has reproduction · 90
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.
PMID 31114675 · PMC6505635 · F1000Research · 2019 · 6 claims · 7 setups
pysradb provides a simple, user-friendly command-line interface for querying metadata and downloading datasets from SRA without requiring knowledge of a programming language.
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Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.
PMID 18632602 · PMC2586155 · Cancer research · 2008 · 8 claims · 7 setups
A novel somatic MEK1 K57N mutation was identified in 2 of 207 primary lung adenocarcinomas
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A sequence-based survey of the complex structural organization of tumor genomes.
PMID 18364049 · PMC2397511 · Genome biology · 2008 · 8 claims · 6 setups
End sequencing profiling (ESP) can identify all classes of genome rearrangements in tumor genomes by paired-end sequencing of BAC clones
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Systems biology in human health and disease.
PMID 17893698 · PMC2013921 · Molecular systems biology · 2007 · 8 claims · 5 setups
High-throughput quantitative proteomics of signaling networks (e.g., HER2 overexpression) can be correlated with biological responses like proliferation and migration to better understand pathways deregulated in cancer.
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Has reproduction · 35
Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.
PMID 32365491 · PMC7281456 · Cancers · 2020 · 8 claims · 7 setups
ZBTB38 expression is decreased in localised prostate cancer and further decreased in metastatic prostate cancer compared to non-cancerous prostate tissue
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Has reproduction · 80
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.
PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups
BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules
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Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.
PMID 19763266 · PMC2740864 · PloS one · 2009 · 8 claims · 8 setups
Androgen treatment alters the whole-cell proteome of LNCaP prostate cancer cells
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Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.
PMID 15836779 · PMC1112590 · BMC genomics · 2005 · 8 claims · 3 setups
A custom 60-mer oligonucleotide microarray covering 3531 secreted and cell surface genes was designed to profile 5 transformed human cell lines and their derivative xenograft tumors.
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Social and ethical implications of genomics, race, ethnicity, and health inequities.
PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups
Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.
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A DNA microarray survey of gene expression in normal human tissues.
PMID 15774023 · PMC1088941 · Genome biology · 2005 · 6 claims · 6 setups
Unsupervised hierarchical clustering of gene expression groups normal tissue samples largely according to anatomic location, cellular composition, or physiologic function.