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).
-
Has reproduction · 68
Multi-scale integrative analyses identify THBS2(+) cancer-associated fibroblasts as a key orchestrator promoting aggressiveness in early-stage lung adenocarcinoma.
PMID 35547750 · PMC9065207 · Theranostics · 2022 · 8 claims · 8 setups
THBS2 is a tumor size-independent biomarker that robustly predicts post-surgical OS and RFS in multiple independent early-stage LUAD cohorts
-
Has reproduction · 100
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.
PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 8 setups
WGCNA-derived gene coexpression modules from breast cancer cell line RNA-seq data correlate significantly with specific cell-shape features
-
Has reproduction · 100
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.
PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups
WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.
-
Has reproduction · 55
Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.
PMID 35901050 · PMC9333241 · PloS one · 2022 · 7 claims · 7 setups
Several WGCNA gene co-expression modules are significantly associated with both LVEF and the DCM phenotype in heart failure patients.
-
Has reproduction · 59
Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.
PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups
Short-term stress and long-term adaptations share common metabolic pathways
-
Has reproduction
A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.
PMID 37936069 · PMC10629022 · BMC genomics · 2023 · 8 claims · 4 setups
Hypersensitive response (HR) accompanied by systemic acquired resistance is the primary contributor to resistance against purple curl leaf disease in agave
-
Has reproduction · 71
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.
PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups
IRG expression pattern clusters LUAD patients into groups with significantly different survival outcomes and immune cell infiltration
-
Has reproduction · 66
STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.
PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 8 claims · 6 setups
Low STAT3 expression in primary PCa is associated with increased OXPHOS and ribosomal biosynthesis at the transcriptomic level
-
Has reproduction · 49
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.
PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups
ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC
-
Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
-
Has reproduction · 92
Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues.
PMID 34056582 · PMC8155268 · Frontiers in artificial intelligence · 2021 · 8 claims · 6 setups
MCF-7 cell lines and human breast cancer tissues show only minimal similarity in biological processes, though some fundamental functions like cell cycle are conserved.
-
Has reproduction · 71
Comprehensive comparison of gene expression diversity among a variety of human stem cells.
PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 8 claims · 8 setups
Tissue origin has a stronger influence on gene expression in iPSCs than in other stem cell types
-
Has reproduction · 84
A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex.
PMID 34253796 · PMC8275748 · Scientific reports · 2021 · 8 claims · 8 setups
The ERV locus HML6_3p21.31c is significantly upregulated in ALS post-mortem motor cortex after multiple-testing correction
-
Has reproduction · 57
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.
PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups
t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes
-
Has reproduction · 69
Machine learning-based identification of an immunotherapy-related signature to enhance outcomes and immunotherapy responses in melanoma.
PMID 39355255 · PMC11442245 · Frontiers in immunology · 2024 · 8 claims · 8 setups
66 consensus immunotherapy prognostic genes (CITPGs) were identified from the intersection of WGCNA modules, immunotherapy responder-vs-non-responder DEGs, and tumor-vs-normal DEGs
-
Full-text index only
Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.
PMID 39775580 · PMC11684664 · PloS one · 2024 · 7 claims · 8 setups
MitoDEGs in MI are mainly involved in mitochondrial function and ATP synthesis pathways
-
Has reproduction · 89
A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.
PMID 32718933 · PMC7467002 · G3 (Bethesda, Md.) · 2020 · 7 claims · 7 setups
There is a general lack of global gene regulation across re-analyzed Wolbachia transcriptomes, with the exception of a weak transcriptional response upregulating ribosomal proteins in early larval stages.
-
Has reproduction · 59
Application of Machine Learning in Predicting Hepatic Metastasis or Primary Site in Gastroenteropancreatic Neuroendocrine Tumors.
PMID 37887568 · PMC10605255 · Current oncology (Toronto, Ont.) · 2023 · 8 claims · 7 setups
Multi-gene random forest models classify primary tumor vs. liver metastasis samples with 100% accuracy in training/test cohorts and >90% accuracy in an independent validation cohort
-
Has reproduction · 66
Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.
PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups
At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls
-
Has reproduction · 88
Vaccine-induced ICOS(+)CD38(+) circulating Tfh are sensitive biosensors of age-related changes in inflammatory pathways.
PMID 34095875 · PMC8149371 · Cell reports. Medicine · 2021 · 8 claims · 8 setups
Vaccine-induced ICOS+CD38+ cTfh from elderly adults show increased TNF-NF-κB pathway transcriptional signaling compared to young adults at day 7 post-vaccination