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 14

System / cell line: consensus ✕ Assay: est ✕ 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
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
A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups

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Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families

pad phylogenetic est est-based
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

est clustered sequences sequence est sequence orf
PigGIS: Pig Genomic Informatics System.

PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups

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PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons

million pig matched wgs blastx repeat sequence
Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

PMID 18655731 · PMC2515324 · BMC genomics · 2008 · 7 claims · 6 setups

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A collection of 132,577 ESTs from four Actinidia species was generated and clustered into 41,858 non-redundant clusters (18,070 TCs and 23,788 singletons)

cdna full-length tentative non-redundant est codon snp
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates.

PMID 17986453 · PMC2238949 · Nucleic acids research · 2008 · 8 claims · 5 setups

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TranspoGene catalogs TEs within protein-coding genes of seven species (human, mouse, chicken, zebrafish, fruit fly, nematode, sea squirt), classified as proximal promoter, exonized, exonic, or intronic TEs.

chicken normal tes genes genomic exon microrna
Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

PMID 17447839 · PMC1853124 · PLoS computational biology · 2007 · 8 claims · 8 setups

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A new algorithm using spliced ESTs (cross-validated against Known Genes and GenBank mRNA) comprehensively maps bidirectional promoters in the human genome

genome transcripts tissues proteins comparative taf250 cpg
Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes.

PMID 18757892 · PMC2553571 · Nucleic acids research · 2008 · 8 claims · 6 setups

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3'-most (L type) poly(A) sites are more conserved than upstream F/M type sites, while intronic (C/H type) sites are the least conserved

consensus poly comparative transposable
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
Polymorphix: a sequence polymorphism database.

PMID 15608242 · PMC540030 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Polymorphix is an ACNUC-structured database that organizes EMBL/GenBank sequences into within-species homologous sequence families using similarity and bibliographic criteria, with alignments, outgroups and phylogenetic trees provided.

eukaryotic clustered consensus aligned sequence blast phylogenetic
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
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 82

An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

exemplar paired-end cleaned assembled transcriptome read novo

Experiments

Characterization of 954 bovine full-CDS cDNA sequences.

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

A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

PigGIS: Pig Genomic Informatics System.

Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates.

Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes.

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

Polymorphix: a sequence polymorphism database.

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

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.