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 20

System / cell line: disease ✕ Assay: fisher's ✕ Clear

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
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
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
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
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
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
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
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
Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

genes candidate simulated alzheimer's genome-wide term null-hypothesis
Somatic mutations of KIT in familial testicular germ cell tumours.

PMID 15150569 · PMC2410291 · British journal of cancer · 2004 · 6 claims · 3 setups

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No germline KIT mutations were found in constitutional DNA from 240 familial TGCT pedigrees

blood ffpe familial csge direct contingency
RummaGEO: Automatic mining of human and mouse gene sets from GEO.

PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

Has reproduction · 63

RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

genes rummageo rummageo-derived leiden bulk gene leiden
Calibrating the performance of SNP arrays for whole-genome association studies.

PMID 18584036 · PMC2432039 · PLoS genetics · 2008 · 8 claims · 7 setups

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Previous SNP array genetic coverage estimates are inflated due to SNP overfitting and sample overfitting, since they were evaluated on the same HapMap SNPs/individuals used to design the arrays.

american liver simulated hapmap snp gene simulation-based
BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

PMID 18234728 · PMC2564862 · Journal of medical genetics · 2008 · 8 claims · 7 setups

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BHD germline mutation detection rate was 88% (51/58 families) using direct DNA sequencing

peripheral blood-derived folliculin chest direct subcloning sequence
PALB2 variants in hereditary and unselected Finnish prostate cancer cases.

PMID 20003494 · PMC2806404 · Journal of negative results in biomedicine · 2009 · 8 claims · 6 setups

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None of the detected PALB2 variants, including 1592delT, show significant association with PRCA at the population level in Finland

blood finnish combined formalin-fixed direct additional statistical
Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis.

PMID 19944577 · PMC2826526 · Artificial intelligence in medicine · 2010 · 8 claims · 5 setups

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The SCOR method outperforms the CCOR method for prioritizing schizophrenia candidate genes

schizophrenia genes ranked gene-based gene expression
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription

Experiments

An online database for brain disease research.

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

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.

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.

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

miRGator: an integrated system for functional annotation of microRNAs.

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.

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

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

Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

Somatic mutations of KIT in familial testicular germ cell tumours.

RummaGEO: Automatic mining of human and mouse gene sets from GEO.

Calibrating the performance of SNP arrays for whole-genome association studies.

BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

PALB2 variants in hereditary and unselected Finnish prostate cancer cases.

Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.