ArticleNucleic acids research2004
The ORFanage: an ORFan database.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- Imported, not invented, genes prevail amongProceedings of the National Academy of Sciences of the United States of America · 2026Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria.Database : the journal of biological databases and curation · 2023Article
- The Lost and Found: Unraveling the Functions of Orphan Genes.Journal of developmental biology · 2023Review
- Antiviral COVID-19 protein and molecular docking:Frontiers in public health · 2022Article
- Review
- Effects of actin-like proteins encoded by two Bacillus pumilus phages on unstable lysogeny, revealed by genomic analysis.Applied and environmental microbiology · 2015Article
- Remote homology and the functions of metagenomic dark matter.Frontiers in genetics · 2015Article
- Synergistic use of plant-prokaryote comparative genomics for functional annotations.BMC genomics · 2011Article
- An evolutionary approach to Function.Journal of biomedical semantics · 2010Article
- A unique group of virus-related, genome-integrating elements found solely in the bacterial family Thermaceae and the archaeal family Halobacteriaceae.Journal of bacteriology · 2010Article
- 'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.The Biochemical journal · 2009Review
- The random nature of genome architecture: predicting open reading frame distributions.PloS one · 2009Article
- A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes.Genome biology · 2009Article
- Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world.Nucleic acids research · 2008Review
- Signature, a web server for taxonomic characterization of sequence samples using signature genes.Nucleic acids research · 2008Article
- Metabolomics.Cell metabolism · 2007Article
- Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function.Journal of bacteriology · 2007Article
- On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer.BMC evolutionary biology · 2006Article
- Computational identification of strain-, species- and genus-specific proteins.BMC bioinformatics · 2005Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As each newly sequenced genome contains a significant number of protein-coding ORFs that are species-, family- or lineage-specific, many interesting questions arise about the evolution and role of these ORFs and of the genomes they are part of. We refer to these poorly conserved ORFs as singleton or paralogous ORFans if they are unique to one genome, or as orthologous ORFans if they appear only in a family of closely related organisms and have no homolog in other genomes. In order to study and classify ORFans we have constructed the ORFanage, an ORFan database. This database consists of the predicted ORFs in fully sequenced microbial genomes, and enables searching for the three types of ORFans in any subset of the genomes chosen by the user. The ORFanage could help in choosing interesting targets for further genomic and evolutionary studies. The ORFanage is accessible via http://www.bioinformatics.buffalo. edu/ORFanage.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.