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 29

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

Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

PMID 18086709 · PMC2241899 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Preferred nucleotide sequences around the initiation codon are diverse among eukaryote species, but differences roughly reflect evolutionary relationships between species

eukaryote genes hexanucleotide saccharomyces comparative cluster hexanucleotide
Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

PMID 18653530 · PMC2528163 · Nucleic acids research · 2008 · 8 claims · 7 setups

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A new computational pipeline identifies trans-SAs using ESTs (not just mRNAs) across 10 animal species, improving coverage over prior methods

est unannotated trans-sa tus computational coding hybridization
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

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

pancreatic computational targeted prevalence snp
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
A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

PMID 17183673 · PMC1762436 · PloS one · 2006 · 8 claims · 7 setups

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HCNCp is a novel invariant (non-variant) cyst protein belonging to a new family of high-cysteine membrane proteins (HCMp) abundant in the Giardia genome

giardia serial northern western
A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes.

PMID 16420688 · PMC1382211 · BMC genomics · 2006 · 7 claims · 4 setups

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PBEC and KC SAGE libraries show approximately 80% overlap in expressed tags, indicating high similarity in gene repertoire

bronchial keratinocytes pbec types sage rt-pcr
The UCSC Genome Browser Database: 2008 update.

PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups

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The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.

zebrafish yale vertebrate non-human sage expression snp
Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

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

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

cervical independent computational long real-time gene
ECgene: genome annotation for alternative splicing.

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

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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
Tissue compartment analysis for biomarker discovery by gene expression profiling.

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

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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
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

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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
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

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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
Genome Network and FANTOM3: assessing the complexity of the transcriptome.

PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

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63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

fantom3 genome large-scale mammalian cage full-length genome
Comparative genomic analysis of prion genes.

PMID 17199895 · PMC1781936 · BMC genomics · 2007 · 8 claims · 8 setups

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SPRN and PRNP homologues are present in all vertebrates, whereas PRND is restricted to tetrapods and PRNT is restricted to primates

vertebrate multi-tissue aligned sprn comparative gene cdna
Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

PMID 18974882 · PMC2570797 · PLoS pathogens · 2008 · 8 claims · 6 setups

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Midgut (oocyst-derived) and salivary gland sporozoite proteomes are markedly different despite near-identical morphology, consistent with their differing hepatocyte infectivity

falciparum berghei nano-lc-ms targeted gene
An integrated genomic analysis of human glioblastoma multiforme.

PMID 18772396 · PMC2820389 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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IDH1 is recurrently mutated at its active site (R132) in 12% of GBM patients, a previously unrecognized alteration in GBM.

gbm additional missense exome targeted snp
A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

PMID 17186946 · PMC1860054 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 8 setups

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Three complementary membrane-enrichment proteomic methods (lectin affinity, biotin/NeutrAvidin affinity, free flow electrophoresis) combined with LC-MS/MS identify 136 transmembrane proteins in human platelets, including many novel ones.

washed platelets tryptic hek293t lc-ms free longsage
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
Chipping away at 'stemness'.

PMID 15287966 · PMC507869 · Genome biology · 2004 · 8 claims · 6 setups

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Global gene-expression analyses across five independent studies identify known and new candidate regulators of human ES-cell growth, self-renewal, and pluripotency.

microarray sage custom
Re-evaluating early breast neoplasia.

PMID 18279539 · PMC2374963 · Breast cancer research : BCR · 2008 · 8 claims · 7 setups

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The classic single linear model of breast cancer progression requires revision based on high-throughput molecular genetic and gene expression data.

dcis breast patient-matched premalignant comparative combined cdna

Experiments

Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

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

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

A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes.

The UCSC Genome Browser Database: 2008 update.

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

ECgene: genome annotation for alternative splicing.

Tissue compartment analysis for biomarker discovery by gene expression profiling.

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

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

Genome Network and FANTOM3: assessing the complexity of the transcriptome.

Comparative genomic analysis of prion genes.

Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

An integrated genomic analysis of human glioblastoma multiforme.

A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

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

Chipping away at 'stemness'.

Re-evaluating early breast neoplasia.