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 34

Assay: sage ✕ 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

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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 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
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
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
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
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
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
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
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
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
Toxoplasma: the next 100years.

PMID 18672085 · PMC2596634 · Microbes and infection · 2008 · 8 claims · 8 setups

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Micronemes, rhoptries, and dense granules are specialized secretory organelles that mediate T. gondii host cell invasion and remodeling

gondii mammalian cdna affymetrix sage
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

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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
Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

PMID 16204454 · PMC1243798 · Nucleic acids research · 2005 · 8 claims · 4 setups

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Cis-encoded natural antisense RNAs show striking preferential complementarity to 3′-UTRs of their target genes in human and mouse genomes

human-mouse model genome-wide comparative computational
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

PMID 15608261 · PMC540076 · Nucleic acids research · 2005 · 8 claims · 7 setups

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GeneTide integrates UniGene, DoTS, AceView, BLAT/GeneLoc genomic alignment, and GeneAnnot probe-set data into a unified Consensus/Uniqueness/Score scheme to associate ESTs with GeneCards genes

transcriptome genome spliced transcripts est genomic splice-orientation
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
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
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
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

Experiments

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

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

Transcriptome annotation using tandem SAGE tags.

The UCSC Genome Browser Database: 2008 update.

ECgene: genome annotation for alternative splicing.

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

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

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

Tissue compartment analysis for biomarker discovery by gene expression profiling.

Chipping away at 'stemness'.

Re-evaluating early breast neoplasia.

Toxoplasma: the next 100years.

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

Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

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

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

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

Comparative genomic analysis of prion genes.