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 15

System / cell line: normal ✕ Assay: tag ✕ Clear

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

Full-text index only

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
Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups

Full-text index only

Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions

normal genome-wide same omim microarray sage computational
DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

Full-text index only

DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

normal dld1 beas2b ramos tss comparative
Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups

Full-text index only

Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia

cervical independent computational long real-time gene
Tissue compartment analysis for biomarker discovery by gene expression profiling.

PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups

Full-text index only

TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures

kidney pure serial rt-pcr sage histo-morphometry
Comparing protein abundance and mRNA expression levels on a genomic scale.

PMID 12952525 · PMC193646 · Genome biology · 2003 · 8 claims · 8 setups

Full-text index only

Correlations between mRNA expression and protein abundance are generally poor or limited across most studies reviewed, including in yeast and human cancers

yeast laser-dissected serum myeloid two-dimensional seldi-tof isotope-coded
Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

PMID 18772397 · PMC2848990 · Science (New York, N.Y.) · 2008 · 8 claims · 6 setups

Full-text index only

Pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations

pancreatic computational targeted prevalence snp
ECgene: genome annotation for alternative splicing.

PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

Full-text index only

ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

brca2 rgs17 organs cdna genomic genome transcript
Contribution of oncoproteomics to cancer biomarker discovery.

PMID 17407558 · PMC1852117 · Molecular cancer · 2007 · 6 claims · 8 setups

Full-text index only

Oncoproteomic biomarker panels (2-DE/MS-based) show higher sensitivity and specificity than currently used single tumor markers across multiple cancer types (Table 1)

serum bladder nipple colorectal 2-de isotope-coded immunoblotting
Integration of cytogenetic landmarks into the draft sequence of the human genome.

PMID 11237021 · PMC7845515 · Nature · 2001 · 8 claims · 6 setups

Full-text index only

7,600 cytogenetically defined landmarks (from a set of 8,877 clones) were placed on the draft sequence of the human genome as a public resource

large-insert bac ml-2 dgap012 fluorescence sts array
Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups

Full-text index only

Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.

serum frozen ig-depleted clinical seldi-tof maldi lc-ms
TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

PMID 15345028 · PMC517934 · BMC medical genetics · 2004 · 8 claims · 4 setups

Full-text index only

No disease-associated mutations were found in TM4SF10 in 16 XLMR patients from 14 families with linkage to the TM4SF10 locus.

genomic dog sage pcr northern sage
Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

PMID 16789823 · PMC1513265 · PLoS genetics · 2006 · 8 claims · 8 setups

Full-text index only

K63-polyubiquitin chain formation protects human cells against translesion synthesis-induced mutations by promoting error-free recovery of blocked replication forks.

a549 western proliferation clonogenic
Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

PMID 19906709 · PMC2811022 · Nucleic acids research · 2010 · 8 claims · 5 setups

Full-text index only

A genome-wide catalog of up to ~9000 overlapping antisense loci (23,782 non-redundant SAT pairs, clustered into 8894) was compiled and stored in the USAGP database

genome affymetrix antisense mirna computational microarray sage
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

Full-text index only

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

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

Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

Tissue compartment analysis for biomarker discovery by gene expression profiling.

Comparing protein abundance and mRNA expression levels on a genomic scale.

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

ECgene: genome annotation for alternative splicing.

Contribution of oncoproteomics to cancer biomarker discovery.

Integration of cytogenetic landmarks into the draft sequence of the human genome.

Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

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