ArticleBMC genomics2004
FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression.
Article in BMC genomics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 45 citations in OpenAlex.
- Molecular Subgroup Classification in Alzheimer's Disease by Transcriptomic Profiles.Journal of molecular neuroscience : MN · 2022Article
- Cardiac physiology and metabolic gene expression during late organogenesis among F. heteroclitus embryo families from crosses between pollution-sensitive and -resistant parents.BMC ecology and evolution · 2022Article
- The effect of short-term hypoxic exposure on metabolic gene expression.Journal of experimental zoology. Part A, Ecological genetics and physiology · 2012Article
- The effects of mitochondrial genotype on hypoxic survival and gene expression in a hybrid population of the killifish, Fundulus heteroclitus.Molecular ecology · 2011Article
- Ecologically and evolutionarily important SNPs identified in natural populations.Molecular biology and evolution · 2011Article
- Gene expression throughout a vertebrate's embryogenesis.BMC genomics · 2011Article
- SNP identification, verification, and utility for population genetics in a non-model genus.BMC genetics · 2010Article
- SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea.Plant methods · 2010Article
- Genomic approaches with natural fish populations.Journal of fish biology · 2010Review
- Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing.Genetica · 2010Article
- The effect of genetic and environmental variation on metabolic gene expression.Molecular ecology · 2009Article
- Technical analysis of cDNA microarrays.PloS one · 2009Article
- Expressed sequence tags (ESTs) from immune tissues of turbot (Scophthalmus maximus) challenged with pathogens.BMC veterinary research · 2008Article
- Local expression of CYP19A1 and CYP19A2 in developing and adult killifish (Fundulus heteroclitus).General and comparative endocrinology · 2008Article
- Fundulus as the premier teleost model in environmental biology: opportunities for new insights using genomics.Comparative biochemistry and physiology. Part D, Genomics & proteomics · 2007Article
- Linking microarray reporters with protein functions.BMC bioinformatics · 2007Article
- ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata.BMC genomics · 2007Article
- Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus.Nature genetics · 2005Article
- Functional genomics of physiological plasticity and local adaptation in killifish.The Journal of heredityArticle
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundWhile studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes.
resultsWe describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus. Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. Steps are taken to ensure that the annotation is self-consistent and that the structure of GO is used to identify higher level functions that may not be annotated directly. An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. In a case study, a set of genes, that had statistically significant regression between gene expression levels and environmental temperature along the Atlantic Coast, shows a statistically significant (P < 0.001) enrichment in genes associated with amine metabolism.
conclusionThe methods described have application for functional genomics studies, particularly among non-model organisms. The web interface for FunnyBase can be accessed at http://genomics.rsmas.miami.edu/funnybase/super_craw4/. Data and source code are available by request at jpaschall@bioinfobase.umkc.edu.
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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.