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 98

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

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

Full-text index only

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
Evolutionary genomics reveals lineage-specific gene loss and rapid evolution of a sperm-specific ion channel complex: CatSpers and CatSperbeta.

PMID 18974790 · PMC2572835 · PloS one · 2008 · 8 claims · 6 setups

Full-text index only

The CatSper channel complex (four CatSpers plus CatSperβ) originated as early as primitive metazoans such as the Cnidarian Nematostella vectensis

metazoan catsper pore chicken tblastn maximum sequence
Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.

PMID 20006904 · PMC2814002 · Neuropeptides · 2010 · 8 claims · 5 setups

Full-text index only

Bioinformatic survey of chicken genome/EST/HTGS databases identifies previously unreported chicken neuropeptide genes

chicken blast microarray est
Mice and more.

PMID 14519193 · PMC328447 · Genome biology · 2003 · 8 claims · 7 setups

Full-text index only

A multispecies weighted conservation score, which accounts for each species' divergence rate, can identify conserved non-coding sequences (multispecies conserved sequences, MCSs) likely to be biologically significant

cftr ciona embryonic chromosome comparative genome bac-based
ECgene: genome annotation for alternative splicing.

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

Full-text index only

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
ECgene: an alternative splicing database update.

PMID 17132829 · PMC1716719 · Nucleic acids research · 2007 · 8 claims · 5 setups

Full-text index only

ECgene provides functional annotation (domain, GO, expression pattern) for alternatively spliced genes

nine genome sage cdna genome-based chi-squared sage
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

PMID 17108355 · PMC1669709 · Nucleic acids research · 2007 · 8 claims · 4 setups

Full-text index only

ASAP II expands human alternative splicing data ~3-fold over the previous ASAP database, to ~89,078 distinct alternative splicing relationships in 11,717 genes

genome animal aligned est genome-wide comparative est
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

Full-text index only

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
ChimerDB--a knowledgebase for fusion sequences.

PMID 16381848 · PMC1347382 · Nucleic acids research · 2006 · 8 claims · 6 setups

Full-text index only

ChimerDB integrates bioinformatics analysis of mRNA/EST sequences, manually collected literature data, and OMIM translocation data into a single fusion sequence knowledgebase

genome candidate pubmed omim blat splice-site ecgene
Twin peaks: the draft human genome sequence.

PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups

Full-text index only

The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.

genome genomic genes yeast whole-genome bac computational
ARED 3.0: the large and diverse AU-rich transcriptome.

PMID 16381826 · PMC1347415 · Nucleic acids research · 2006 · 7 claims · 6 setups

Full-text index only

ARED 3.0 computationally mapped more than 4000 ARE-mRNAs to the human genome, representing 5-8% of human genes.

records est est-derived combined computational est sequence
Non-EST based prediction of exon skipping and intron retention events using Pfam information.

PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

Full-text index only

A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

refseq dbest genome pfam initio est comparative
The revolution of the biology of the genome.

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

Full-text index only

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

genome drosophila schizosaccharomyces gene est mount comparative
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

Full-text index only

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
Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

PMID 16925839 · PMC1810554 · Genome biology · 2006 · 7 claims · 5 setups

Full-text index only

Pairagon+N-SCAN_EST, using only native alignments, was as accurate as ENSEMBL and ExoGean in the EGASP mRNA/EST evidence assessment

encode genome cdna-to-genome novo comparative
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

PMID 16925833 · PMC1810548 · Genome biology · 2006 · 8 claims · 5 setups

Full-text index only

AUGUSTUS predicted significantly more genes correctly than any other ab initio program in EGASP

genome human-mouse genes initio comparative extrinsic
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

PMID 17202160 · PMC1899096 · Nucleic acids research · 2007 · 7 claims · 5 setups

Full-text index only

PolyA_DB 2 catalogs poly(A) sites for genes in human, mouse, rat, chicken and zebrafish, identified by aligning cDNA/ESTs with genome sequences

sequences poly cdna trace pssm-based
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

Full-text index only

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
Evolutionarily conserved human targets of adenosine to inosine RNA editing.

PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

Full-text index only

Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

panel brain chicken flna comparative rt-pcr homology
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

Full-text index only

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

Experiments

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

Evolutionary genomics reveals lineage-specific gene loss and rapid evolution of a sperm-specific ion channel complex: CatSpers and CatSperbeta.

Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.

Mice and more.

ECgene: genome annotation for alternative splicing.

ECgene: an alternative splicing database update.

The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

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

ChimerDB--a knowledgebase for fusion sequences.

Twin peaks: the draft human genome sequence.

ARED 3.0: the large and diverse AU-rich transcriptome.

Non-EST based prediction of exon skipping and intron retention events using Pfam information.

The revolution of the biology of the genome.

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

Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

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

Evolutionarily conserved human targets of adenosine to inosine RNA editing.

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