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 26

System / cell line: tissues ✕ Assay: coding ✕ Clear

'Genome design' model and multicellular complexity: golden middle.

PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

normal genes proteins encoded oligonucleotide gene functional
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

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GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

chromosome genomic comparative phylohmmcons conserved
DDBJ in collaboration with mass-sequencing teams on annotation.

PMID 15608189 · PMC539974 · Nucleic acids research · 2005 · 7 claims · 5 setups

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DDBJ collected and released 1,066,084 entries (718,072,425 bases) in the past year, including the complete chimpanzee chromosome 22 sequence and silkworm whole-genome shotgun data

chimpanzee silkworm mus homo whole-chromosome whole-genome cage
The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.

PMID 18948287 · PMC2686472 · Nucleic acids research · 2009 · 8 claims · 5 setups

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fRNAdb 3.0 is a completely rebuilt sequence database hosting a much larger collection of known/predicted non-coding RNA sequences with improved search functionality

non-coding frnadb-hosted genomic mammalian sequence genome blastn
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
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

genome transcriptome gene genes full-length genome cdna
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

Has reproduction · 76

The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

pyronema confluens fungal whole-genome k-mer rna-seq
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups

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miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.

conserved putative mirna-target normal comparative machine mirna
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

PMID 18029362 · PMC2238982 · Nucleic acids research · 2008 · 8 claims · 6 setups

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miRNAMap 2.0 is a resource collecting experimentally verified miRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes

major tissues conserved predicted quantitative bead-based microarray
Adverse prognosis of epigenetic inactivation in RUNX3 gene at 1p36 in human pancreatic cancer.

PMID 18475302 · PMC2391125 · British journal of cancer · 2008 · 7 claims · 5 setups

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RUNX3 promoter hypermethylation is frequent in primary pancreatic cancer tissue

pancreatic microsatellite methylation-specific bisulphite
A critical reassessment of the role of mitochondria in tumorigenesis.

PMID 16187796 · PMC1240051 · PLoS medicine · 2005 · 8 claims · 8 setups

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A significant number of published medical mtDNA cancer studies are based on obviously flawed sequencing results.

hepatocellular papillary prostate tissues mtdna mutational
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

Has reproduction · 50

Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.

gossypium transcripts uq-normalized differentially comparative coding bulk
Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

PMID 24304889 · PMC3964963 · Nucleic acids research · 2014 · 8 claims · 6 setups

Has reproduction · 84

Expression Atlas is a value-added database providing gene, protein and splice variant expression across cell types, organism parts, developmental stages, diseases and other biological/experimental conditions, built from manually curated high-quality microarray and RNA-sequencing experiments from ArrayExpress.

organisms arrayexpress-derived pride rna-sequencing single-channel two-colour
Widespread ectopic expression of olfactory receptor genes.

PMID 16716209 · PMC1508154 · BMC genomics · 2006 · 8 claims · 6 setups

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OR genes show widespread, locus-dependent, heterogeneous ectopic expression across dozens of non-olfactory human and mouse tissues

tissues olfactory intact probesets microarray est custom
Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.

PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups

Has reproduction · 23

The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies

adriatic mitochondrial autosomal brain whole-genome phylogenetic d-statistics
Organismal complexity, cell differentiation and gene expression: human over mouse.

PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

human-mouse oligonucleotide exon comparative
Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

PMID 18834967 · PMC2561938 · American journal of human genetics · 2008 · 7 claims · 6 setups

Has reproduction · 70

Heterozygous CHD7 mutations cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome without the CHARGE phenotype.

ihh additional chd7 sanger targeted rt-pcr
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

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MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

genome tissues novo pairwise rt-pcr
The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

PMID 12036445 · PMC5927037 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 5 setups

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SNI (elevated spontaneous point mutation rate without microsatellite instability) is present in rat mammary carcinoma cell lines and human breast cancer cell lines

mammary same normal pcr-sscp direct quantitative
Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.

PMID 15447792 · PMC523852 · BMC medical genetics · 2004 · 8 claims · 8 setups

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TMPRSS3 mutations were identified in four additional Pakistani families with recessive, nonsyndromic congenital deafness co-segregating with DFNB8/B10 haplotypes

pakistani affected retina tissues linkage sanger race

Experiments

'Genome design' model and multicellular complexity: golden middle.

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

DDBJ in collaboration with mass-sequencing teams on annotation.

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.

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

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

Adverse prognosis of epigenetic inactivation in RUNX3 gene at 1p36 in human pancreatic cancer.

A critical reassessment of the role of mitochondria in tumorigenesis.

Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

Widespread ectopic expression of olfactory receptor genes.

Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.

Organismal complexity, cell differentiation and gene expression: human over mouse.

Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.