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 169

System / cell line: analysis ✕ Assay: cluster ✕ Clear

iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype.

PMID 19674965 · PMC2773724 · Molecular & cellular proteomics : MCP · 2009 · 6 claims · 5 setups

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Serial transplantation of human GBM xenografts in nude rats converts an initially highly infiltrative, non-angiogenic phenotype into a highly angiogenic phenotype over 4-6 generations.

membrane-enriched xenograft homogenate quantified itraq western bradford
Proteome analysis enables separate clustering of normal breast, benign breast and breast cancer tissues.

PMID 12865921 · PMC2394238 · British journal of cancer · 2003 · 6 claims · 3 setups

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Hierarchical cluster analysis of 2-DE proteome data can distinguish normal breast, benign breast, and breast cancer tissues based on protein expression profiles

breast two-dimensional hierarchical mann-whitney
Single-cell multiomics analysis of chronic myeloid leukemia links cellular heterogeneity to therapy response.

PMID 39503729 · PMC11540304 · eLife · 2024 · 8 claims · 5 setups

Has reproduction · 75

CITE-seq multiomics reveals that each CML patient harbors a unique composition of stem and progenitor cells at diagnosis

lin-cd34+ cml cite-seq facs differential
Protein expression patterns in primary carcinoma of the vagina.

PMID 15199389 · PMC2409807 · British journal of cancer · 2004 · 5 claims · 4 setups

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Cluster analysis of 2-DE proteomic data allows accurate discrimination between normal vaginal mucosa, primary vaginal carcinoma and primary cervical carcinoma

fresh-frozen excised normal same two-dimensional matrix-assisted hierarchical
CLEAN: CLustering Enrichment ANalysis.

PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

four breast combined hierarchical cluster csimm-based
An analysis of human microRNA and disease associations.

PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups

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MicroRNAs tend to show similar dysfunctional evidence (both up- or both down-regulated) for diseases within the same disease cluster, and different dysfunctional evidence between different disease clusters.

literature-derived diseases mirnas mirna literature bipartite mirna
Clustering by neurocognition for fine mapping of the schizophrenia susceptibility loci on chromosome 6p.

PMID 19694819 · PMC4286260 · Genes, brain, and behavior · 2009 · 6 claims · 6 setups

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A family-based clustering strategy using neurocognitive test scores (CPT, WCST) can identify more homogeneous subgroups of schizophrenia families for genetic association analysis

multiplex affected subjects cluster-specific family-based continuous wisconsin
Comparative genomic analysis of Campylobacter jejuni associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity.

PMID 17919333 · PMC2174954 · BMC genomics · 2007 · 8 claims · 4 setups

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GBS/MFS strains are genomically heterogeneous, falling into about six major lineages rather than a single clonal group

jejuni subset matched comparative fisher's hierarchical
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

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Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

caninum ceylanicum est bioinformatic functional
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

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The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

non-identical gene3d cath whole-gene domain transmembrane
Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.

PMID 37133905 · PMC10272873 · Microbial genomics · 2023 · 8 claims · 8 setups

Has reproduction · 92

cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.

jejuni same subset isolate cgmlst hqsnp genome
Oligomeric protein structure networks: insights into protein-protein interactions.

PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization

non-redundant same known complexes structure hub comparison
The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups

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P-POD is the first comparative genomics database to combine results from multiple computational ortholog/homolog prediction methods with manually curated literature-derived experimental evidence of functional conservation.

sequences orthomcl yeast orthomcl jaccard phylogenetic
A taxonomy of epithelial human cancer and their metastases.

PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

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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

epithelial tumor metastatic breast microarray gene fisher
Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 6 claims · 8 setups

Has reproduction

A deep learning WSI cluster (three-class mini batch K-means on Inception V3 features) is associated with overall survival (P<0.001) and is an independent prognostic predictor (P=0.031) in BLCA.

tcga-blca blca tcga deep transfer-learning neural-network
Inferring combinatorial regulation of transcription in silico.

PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

upstream monocytes same tfbs microarray permutation
Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.

PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups

Has reproduction · 69

Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis

colon gut single-cell 16s western
Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.

PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups

Has reproduction · 75

AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles

post-mortem brain zebrafish bulk single-cell unsupervised
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 · 7 claims · 8 setups

Has reproduction · 71

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

bca meta-geo tcga-blca tcga bulk rna-seq somatic

Experiments

iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype.

Proteome analysis enables separate clustering of normal breast, benign breast and breast cancer tissues.

Single-cell multiomics analysis of chronic myeloid leukemia links cellular heterogeneity to therapy response.

Protein expression patterns in primary carcinoma of the vagina.

CLEAN: CLustering Enrichment ANalysis.

An analysis of human microRNA and disease associations.

Clustering by neurocognition for fine mapping of the schizophrenia susceptibility loci on chromosome 6p.

Comparative genomic analysis of Campylobacter jejuni associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.

Oligomeric protein structure networks: insights into protein-protein interactions.

The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

A taxonomy of epithelial human cancer and their metastases.

Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

Inferring combinatorial regulation of transcription in silico.

Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.

Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.

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