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 32

System / cell line: disease ✕ Assay: exact ✕ Clear

Mapping proteins to disease terminologies: from UniProt to MeSH.

PMID 18460185 · PMC2367626 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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Developed a three-step procedure (disease name extraction, exact matching, partial/similarity-based matching) to map UniProtKB/Swiss-Prot disease names to MeSH terms

randomly swiss-prot uniprotkb mesh manual exact partial
Screening large-scale association study data: exploiting interactions using random forests.

PMID 15588316 · PMC545646 · BMC genetics · 2004 · 7 claims · 3 setups

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Random forest importance measure significantly outperforms the Fisher Exact test as a screening tool when risk SNPs interact.

simulated same simulation random fisher
Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

PMID 18545673 · PMC2409220 · PloS one · 2008 · 8 claims · 6 setups

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An integrative ad-hoc functional GO analysis combining threshold-based (Fisher exact/hypergeometric) and threshold-free (Kolmogorov-Smirnov) statistics, plus term-to-parent comparisons, detects disease-relevant splicing events from exon array data.

mg-thymoma colon exon fluorescent reverse
Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

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Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

biomedical refseq training independent text-mining data-mining candidate
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

user-supplied ranked gene fasta-formatted functional gene novo
Glycomics and disease markers.

PMID 19775929 · PMC2788081 · Current opinion in chemical biology · 2009 · 8 claims · 7 setups

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Over 70% of all human proteins are glycosylated

serum glycoprotein-derived sera maldi-fticr glycan nanoflow
Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.

PMID 19744994 · PMC2773259 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 5 setups

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560 genetic skin diseases can be decomposed into 71 elementary phenotypic features (42 dermatologic, 29 systemic) that combine to represent each disease as a point in a multidimensional phenotype space

genodermatoses phenotype disease gene-phenotype manual correlation principal
Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies.

PMID 19073697 · PMC2632920 · Nucleic acids research · 2009 · 8 claims · 5 setups

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Combining high protein-interaction network scores with significant PID-related GO terms identifies novel PID candidate genes

immunome known protein-interaction gene comparative
Association of GSK3B with Alzheimer disease and frontotemporal dementia.

PMID 18852354 · PMC2841136 · Archives of neurology · 2008 · 8 claims · 5 setups

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The GSK3B intronic polymorphism IVS2-68G>A is associated with increased risk of AD and FTD in a case-control cohort

genomic case-control family-based sib-pair pcr allele-specific fluorescence-polarization
An online database for brain disease research.

PMID 16594998 · PMC1489945 · BMC genomics · 2006 · 7 claims · 5 setups

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SMRIDB is a comprehensive web-based database integrating gene expression data and clinical metadata to aid understanding of the genetic effects of brain disease (bipolar disorder, schizophrenia, depression)

postmortem individual disease studies microarray array gene-by-gene
Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

PMID 34297416 · PMC8766893 · Neuropathology and applied neurobiology · 2022 · 8 claims · 5 setups

Has reproduction · 92

Systematic review of 306 eligible articles identified 196 distinct proteins constituting the ADRA (AD reactive astrocyte) protein set

post-mortem adra immunohistochemistry protein-protein pathway
CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

PMID 15507145 · PMC526769 · BMC medical genetics · 2004 · 8 claims · 7 setups

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PCR amplification and sequencing of CLC-2 revealed 1 SNP in the promoter, 4 SNPs in intron 1, and none in exon 20

nasal genomic ib3-1 western pcr fisher's
Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

PMID 16824219 · PMC1534050 · BMC neurology · 2006 · 7 claims · 5 setups

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The C282Y variant allele of HFE is significantly overrepresented in PD patients compared to controls, suggesting it confers higher risk for PD

genomic same pooled pcr-rflp pcr-based cross-tabulation
The role of positive selection in determining the molecular cause of species differences in disease.

PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals

orthologous omim meta-database panther comparative disease protein-protein
miRGator: an integrated system for functional annotation of microRNAs.

PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

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miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

genome predicted tissues organs computational functional mirna
HFE H63D mutation frequency shows an increase in Turkish women with breast cancer.

PMID 16503999 · PMC1402308 · BMC cancer · 2006 · 6 claims · 2 setups

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HFE H63D allele frequency is significantly higher in Turkish breast cancer patients (22.2%) than in healthy controls (14%)

archived same pcr-rflp statistical
Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE).

PMID 15339345 · PMC517707 · BMC bioinformatics · 2004 · 7 claims · 5 setups

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A Bayesian mixture model is proposed to account for within-class biological variability in SAGE/Digital-Northern/MPSS tag counting data.

astrocytoma same sage classical beta-binomial
Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

PMID 19039135 · PMC2746051 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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Diagnosis and relapse ALL samples show different patterns of CNAs, with relapse-acquired abnormalities preferentially affecting cell cycle regulation and B-cell development genes

matched bone leukemia diagnosis snp flow quantitative
Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups

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Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window

pooled computational identified additional label-free lspad pathway-associated
A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups

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A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.

kidney same identified additional microarray significance fisher's

Experiments

Mapping proteins to disease terminologies: from UniProt to MeSH.

Screening large-scale association study data: exploiting interactions using random forests.

Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

Glycomics and disease markers.

Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.

Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies.

Association of GSK3B with Alzheimer disease and frontotemporal dementia.

An online database for brain disease research.

Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

The role of positive selection in determining the molecular cause of species differences in disease.

miRGator: an integrated system for functional annotation of microRNAs.

HFE H63D mutation frequency shows an increase in Turkish women with breast cancer.

Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE).

Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.