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).
-
Full-text index only
mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.
PMID 18980691 · PMC2612029 · BMC genomics · 2008 · 8 claims · 8 setups
mtDNA depletion confers specific, shared gene expression profiles in A549 cells grown in culture and as xenografts
-
Full-text index only
Use of functional genomics to understand influenza-host interactions.
PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups
Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques
-
Full-text index only
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.
-
Full-text index only
Delineation of a gene network underlying the pulmonary response to oxidative stress in asthma.
PMID 19730131 · PMC3328512 · Journal of investigative medicine : the official publication of the American Federation for Clinical Research · 2009 · 8 claims · 6 setups
Integration of multiple public microarray datasets via a four-way Venn diagram identifies genes commonly expressed in asthma- and cigarette smoke-exposed lung
-
Has reproduction · 53
PulmonDB: a curated lung disease gene expression database.
PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 6 claims · 6 setups
PulmonDB is a curated, web-based gene expression database and R package integrating microarray and RNA-seq data for COPD and IPF with manually curated controlled-vocabulary annotation.
-
Has reproduction · 80
Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.
PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups
WGCNA identified 214 key genes in the blue module most correlated with LUAD
-
Has reproduction
Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.
PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups
The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells
-
Has reproduction · 88
Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.
PMID 37954334 · PMC10637964 · Heliyon · 2023 · 8 claims · 8 setups
APOBEC family genes are aberrantly expressed across cancers, with APOBEC3B the most consistently upregulated, and APOBEC3B/APOBEC3A are markedly altered in LUAD
-
Full-text index only
A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes.
PMID 16420688 · PMC1382211 · BMC genomics · 2006 · 7 claims · 4 setups
PBEC and KC SAGE libraries show approximately 80% overlap in expressed tags, indicating high similarity in gene repertoire
-
Has reproduction · 93
Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.
PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups
5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)
-
Has reproduction · 90
Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.
PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups
Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)
-
Has reproduction · 71
Targeted and personalized immunotherapy in lung adenocarcinoma: single-cell RNA sequencing of MAFF+ tumor cells and the therapeutic potential of FOS.
PMID 40936936 · PMC12420628 · Frontiers in immunology · 2025 · 7 claims · 8 setups
A highly stem-like C0 MAFF+ tumor cell subtype dominates invasive LUAD, producing chemokines and activating lipid metabolism
-
Has reproduction · 100
Betacoronavirus-specific alternate splicing.
PMID 35074468 · PMC8782732 · Genomics · 2022 · 8 claims · 8 setups
Genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those in SARS-CoV and MERS, affecting a diverse set of genes and biological functions related to virus biology.
-
Has reproduction · 71
Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.
PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 7 claims · 8 setups
CAI is positively correlated with translational efficiency, supporting its use as a proxy for viral mRNA translation in cell types.
-
Has reproduction · 95
Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.
PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups
Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity