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 60

System / cell line: est ✕ Assay: comparison ✕ Clear

Characterization of 954 bovine full-CDS cDNA sequences.

PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

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954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

bovine translated bflic sequence est primer-walking blastp
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays.

PMID 19906711 · PMC2808952 · Nucleic acids research · 2010 · 6 claims · 4 setups

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PLANdbAffy is a database of Affymetrix probe alignments to the human genome for five widely used arrays (HG-U133A, HG-U133B, HG-U133 Plus 2.0, Human Exon 1.0, Human Gene 1.0)

hg-u133a ucsc dbsnp probe blat est snp
Identification and characterization of insect-specific proteins by genome data analysis.

PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

drosophila insect-core locusta insect-specific comparative est functional
Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

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A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

genomes longin plant phytolongin iterative phylogenetic genomic
The revolution of the biology of the genome.

PMID 15040884 · PMC7091781 · Cell research · 2004 · 8 claims · 6 setups

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Polyploidization and gene duplication are the major mechanisms increasing eukaryotic genome size.

genome drosophila schizosaccharomyces gene est mount comparative
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous
Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

redundant mammalian genomic vertebrates blast pattern-hit tblastn
Network-assisted protein identification and data interpretation in shotgun proteomics.

PMID 19690572 · PMC2736651 · Molecular systems biology · 2009 · 7 claims · 7 setups

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Confidently identified proteins in a sample form tightly connected sub-networks in the protein interaction network, with significantly higher clustering coefficients than random or topology-matched random sub-networks.

yeast organs mammary organ shotgun clique-enrichment microarray
The global landscape of sequence diversity.

PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups

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Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.

fully eukaryotic complete gene blast-based est 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
Mining expressed sequence tags identifies cancer markers of clinical interest.

PMID 17078886 · PMC1635568 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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An EST-mining approach (Fisher Exact Test on tumor vs. non-tumor library hit counts) identifies differentially expressed transcripts with an estimated false discovery rate below 22% when human and mouse screens are combined.

dbest cancer gene est human-mouse leave-one-out
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

PMID 17201911 · PMC1774567 · BMC genomics · 2007 · 8 claims · 5 setups

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A computational EST-based pipeline can identify UTR-SNPs that are statistically over-represented in cancerous versus normal tissue libraries

est acute 100-nt whole-genome est-based pcr-based secondary
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

genome poly est cdna est blast cdna
A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

PMID 16237125 · PMC1258171 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A genome-wide computational survey identifies 245 genes in mammals (264 across six species) that produce RREO events in expressed sequences

expressed representative random genes computational orf statistical
Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

muscle-specific bovine refseq cardiac novo est blastn
Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

PMID 17386095 · PMC1868932 · Genome biology · 2007 · 8 claims · 4 setups

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More than 55,000 totally intronic noncoding (TIN) RNAs are transcribed from the introns of 74% of unique RefSeq genes.

dbest liver cultures refseq est oligoarray polymerase
A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

PMID 19852815 · PMC2771047 · BMC genomics · 2009 · 8 claims · 5 setups

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The Conditional Stepped Reciprocal Best Hit (CSRBH) approach, combining direct RBH and zebrafish-stepped RBH (SRBH), outperformed other ortholog assignment methods and attained 8,726 carp-human functional homolog relationships for 16,650 carp contigs

carp randomly zebrafish reciprocal sequence microarray
HaploSNPer: a web-based allele and SNP detection tool.

PMID 18307806 · PMC2288614 · BMC genetics · 2008 · 6 claims · 2 setups

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HaploSNPer is a web-based tool integrating BLASTN, CAP3/PHRAP, and QualitySNP into a single pipeline for allele and SNP detection from diploid and polyploid species

sncg wheat est
Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

PMID 12783626 · PMC161800 · BMC genomics · 2003 · 8 claims · 5 setups

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A comparative genomics approach using hamster testis cDNA sequencing can identify genes not previously annotated in the human, mouse, rat and Fugu genomes

hamster testis predicted cdna northern comparative
Lack of involvement of known DNA methyltransferases in familial hydatidiform mole implies the involvement of other factors in establishment of imprinting in the human female germline.

PMID 12546714 · PMC149328 · BMC genetics · 2003 · 8 claims · 5 setups

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A human oocyte-specific DNMT1 isoform (DNMT1o), driven by a novel upstream exon 1o, is expressed in mature oocytes and early embryos but not in somatic tissues

oocytes genomic fbhm population rt-pcr est direct

Experiments

Characterization of 954 bovine full-CDS cDNA sequences.

PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays.

Identification and characterization of insect-specific proteins by genome data analysis.

Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

The revolution of the biology of the genome.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

Network-assisted protein identification and data interpretation in shotgun proteomics.

The global landscape of sequence diversity.

ECgene: genome annotation for alternative splicing.

Mining expressed sequence tags identifies cancer markers of clinical interest.

In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

HaploSNPer: a web-based allele and SNP detection tool.

Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

Lack of involvement of known DNA methyltransferases in familial hydatidiform mole implies the involvement of other factors in establishment of imprinting in the human female germline.