ArticleNucleic acids research2009
Pseudofam: the pseudogene families database.
Article in Nucleic acids research, 2009. 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, 46 citations in OpenAlex.
- Functional roles and clinical implications of pseudogenes signatures as emerging biomarkers in cancer.Discover oncology · 2026Review
- Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance.Applied microbiology and biotechnology · 2024Review
- Low expression of PEBP1P2 promotes metastasis of clear cell renal cell carcinoma by post-transcriptional regulation of PEBP1 and KLF13 mRNA.Experimental hematology & oncology · 2022Article
- ANXA2P2: A Potential Immunological and Prognostic Signature in Ovarian Serous CystadenocarcinomaFrontiers in oncology · 2022Article
- GENCODE Pseudogenes.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Pseudogenes: Four Decades of Discovery.Methods in molecular biology (Clifton, N.J.) · 2021Article
- FTH1 Pseudogenes in Cancer and Cell Metabolism.Cells · 2020Review
- Transcriptional activity and strain-specific history of mouse pseudogenes.Nature communications · 2020Article
- Pseudo2GO: A Graph-Based Deep Learning Method for Pseudogene Function Prediction by Borrowing Information From Coding Genes.Frontiers in genetics · 2020Article
- Genomics and data science: an application within an umbrella.Genome biology · 2019Review
- PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers.GigaScience · 2019Article
- Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes.Scientific reports · 2017Article
- Review
- Pseudogenes and Their Genome-Wide Prediction in Plants.International journal of molecular sciences · 2016Review
- Characterization of human pseudogene-derived non-coding RNAs for functional potential.PloS one · 2014Article
- AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource.Database : the journal of biological databases and curation · 2014Article
- Evolution of SH2 domains and phosphotyrosine signalling networks.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2012Review
- Article
- Non-coding RNAs as regulators of gene expression and epigenetics.Cardiovascular research · 2011Review
- Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.Molecular vision · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Pseudofam (http://pseudofam.pseudogene.org) is a database of pseudogene families based on the protein families from the Pfam database. It provides resources for analyzing the family structure of pseudogenes including query tools, statistical summaries and sequence alignments. The current version of Pseudofam contains more than 125,000 pseudogenes identified from 10 eukaryotic genomes and aligned within nearly 3000 families (approximately one-third of the total families in PfamA). Pseudofam uses a large-scale parallelized homology search algorithm (implemented as an extension of the PseudoPipe pipeline) to identify pseudogenes. Each identified pseudogene is assigned to its parent protein family and subsequently aligned to each other by transferring the parent domain alignments from the Pfam family. Pseudogenes are also given additional annotation based on an ontology, reflecting their mode of creation and subsequent history. In particular, our annotation highlights the association of pseudogene families with genomic features, such as segmental duplications. In addition, pseudogene families are associated with key statistics, which identify outlier families with an unusual degree of pseudogenization. The statistics also show how the number of genes and pseudogenes in families correlates across different species. Overall, they highlight the fact that housekeeping families tend to be enriched with a large number of pseudogenes.
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.