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).

Publications 1.3k Datasets 392.5k Experiments 19

System / cell line: qpcr ✕ Assay: wgcna ✕ Clear

Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

PMID 32714363 · PMC7344232 · Frontiers in genetics · 2020 · 6 claims · 6 setups

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The midnight blue module and the yellow module play vital roles in the pathogenesis of CAD in non-diabetic patients

pbmcs blood apoe genes microarray rt-qpcr elisa
Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.

PMID 41809777 · PMC12968932 · Translational andrology and urology · 2026 · 8 claims · 8 setups

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A 37-GSRlncRNA prognostic signature stratifies BLCA patients into low- and high-risk groups with significant differences in survival, pathway enrichment, immune infiltration, and mutational profiles

tcga-blca blca paired wgcna differential machine
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

Has reproduction · 80

WGCNA identified 214 key genes in the blue module most correlated with LUAD

tcga-luad merged tedc2-associated a549 wgcna differential machine
Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

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Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

luad demtdmrgs gse131907 wgcna kegg univariate
PVT1 lincRNA signals an androgen-dependent transcriptional activation program of oncogenes in prostate cancer cells.

PMID 41792045 · PMC13139993 · International journal of cancer · 2026 · 8 claims · 7 setups

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PVT1 knockdown significantly reduces LNCaP cell proliferation and increases sensitivity to apoptosis

lncap tcga-prad rt-qpcr trypan transwell
Targeting TPX2-dependent lineage plasticity by CDK4/6 inhibition reverses therapy resistance in neuroendocrine bladder carcinoma.

PMID 41923619 · PMC13130694 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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A 315-gene 'NE-like signature' (NE-like Sig), derived from the WGCNA MEmidnightblue module, marks a lineage-plasticity-associated transcriptional program distinct from canonical NE differentiation.

cases in-house bladder nebc wgcna single-cell spatial
A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.

PMID 37936069 · PMC10629022 · BMC genomics · 2023 · 8 claims · 4 setups

Has reproduction

Hypersensitive response (HR) accompanied by systemic acquired resistance is the primary contributor to resistance against purple curl leaf disease in agave

agave bulk wgcna qpcr
Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation.

PMID 41939867 · PMC13043422 · Frontiers in immunology · 2026 · 7 claims · 8 setups

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CXCL13, IL33, TLR4, and IGF1 are core IPF genes consistently linked to immune infiltration and fibrotic remodeling across bulk, single-cell, spatial, and blood multi-omics data

lung candidate bulk normalized bulk ppi machine
Integrating co-expression network analysis and machine learning to reveal the regulatory landscape of GPD genes in Chlamydomonas reinhardtii under salinity stress.

PMID 42004709 · PMC13089224 · PeerJ · 2026 · 8 claims · 8 setups

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GPD2 and GPD3 cluster into distinct WGCNA co-expression modules (magenta and black, respectively) with contrasting temporal expression profiles

chlamydomonas genes normalized gpd bulk weighted gene
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups

Has reproduction · 55

352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples

endometrial degs hub decidua microarray wgcna machine
Identify GDPD3 as a key regulator of epithelial-mesenchymal transition and prostate adenocarcinoma progression via the LPA/LPAR1/AKT axis: transcriptomic and experimental study.

PMID 41562071 · PMC12813044 · Frontiers in immunology · 2025 · 7 claims · 8 setups

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GDPD3 is upregulated in PRAD tumor tissue and its knockdown inhibits tumor cell proliferation, invasion, and migration

prad tcga-prad du145 scrna-seq bulk wgcna
Uncovering the transcriptional landscape of estrogen-induced gonadal feminization in the Chinese giant salamander.

PMID 41808025 · PMC13085422 · BMC genomics · 2026 · 8 claims · 7 setups

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E2 exposure induces male-to-female gonadal sex reversal in CGS, confirmed by histological evidence across developmental stages.

gonadal tail-tip deg candidate rna-seq histology rt-qpcr
Identification and validation of key PANoptosis-related genes via integrative machine learning and single-cell sequencing in AILI.

PMID 41858622 · PMC12995703 · iScience · 2026 · 8 claims · 8 setups

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Cdkn1a and Pdk1 are key PANoptosis-related genes with high diagnostic potential for AILI

liver training bulk wgcna machine
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

Has reproduction · 71

Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

meta-geo tcga-blca bca genomics unsupervised lasso weighted
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

Has reproduction · 49

ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC

ptc degs key bulk kegg weighted
LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.

PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 8 claims · 8 setups

Has reproduction · 49

LRP1 is a hub gene with the highest diagnostic performance among 30 candidate hub genes identified by machine learning

ectopic geo gse5108 training microarray wgcna machine
Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.

PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups

Has reproduction · 86

RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.

peripheral demrnas blood thp-1 rna-seq annotation wgcna
Smoking promotes colorectal cancer via the CKAP2L/AREG axis.

PMID 41823522 · PMC13038336 · International journal of oncology · 2026 · 8 claims · 8 setups

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Smoking is positively associated with CRC risk, confirmed by both cross-sectional (NHANES) and Mendelian randomization analyses

participants european crc hct116 cross-sectional two-sample single-cell
Characteristics of Burkholderia pyrrocinia and the biocontrol mechanism by which it affects lily bulb rot caused by F. oxysporum.

PMID 42112433 · PMC13149453 · Frontiers in microbiology · 2026 · 7 claims · 8 setups

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Strain YFLYS026 was isolated from lily rhizosphere soil and identified as Burkholderia pyrrocinia via 16S rDNA/gyrB sequencing and phylogenetics

phytopathogenic oxysporum tissue-cultured lily plate double-plate pot

Experiments

Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.

Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.

Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

PVT1 lincRNA signals an androgen-dependent transcriptional activation program of oncogenes in prostate cancer cells.

Targeting TPX2-dependent lineage plasticity by CDK4/6 inhibition reverses therapy resistance in neuroendocrine bladder carcinoma.

A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.

Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation.

Integrating co-expression network analysis and machine learning to reveal the regulatory landscape of GPD genes in Chlamydomonas reinhardtii under salinity stress.

Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

Identify GDPD3 as a key regulator of epithelial-mesenchymal transition and prostate adenocarcinoma progression via the LPA/LPAR1/AKT axis: transcriptomic and experimental study.

Uncovering the transcriptional landscape of estrogen-induced gonadal feminization in the Chinese giant salamander.

Identification and validation of key PANoptosis-related genes via integrative machine learning and single-cell sequencing in AILI.

Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.

Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.

Smoking promotes colorectal cancer via the CKAP2L/AREG axis.

Characteristics of Burkholderia pyrrocinia and the biocontrol mechanism by which it affects lily bulb rot caused by F. oxysporum.