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 10

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

Transcriptome annotation using tandem SAGE tags.

PMID 17709346 · PMC2034470 · Nucleic acids research · 2007 · 8 claims · 7 setups

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A novel algorithm pairs tandem SAGE tags anchored on two different restriction sites (CATG and GATC) to define tag-delimited genomic sequences (TDGS)

monocyte-derived unigene genome macrophage sage modified virtual
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
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

lncap lncap-derived r1881-treated massively blast blat
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
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
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
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
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
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
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

Experiments

Transcriptome annotation using tandem SAGE tags.

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

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

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

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

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

Comparative genomic analysis of prion genes.

An integrated genomic analysis of human glioblastoma multiforme.

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

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.