FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression

Paschall, Justin E.; Oleksiak, Marjorie F.; VanWye, Jeffrey D.; Roach, Jennifer L.; Whitehead, J. Andrew; Wyckoff, Gerald J.; Kolell, Kevin J.; Crawford, Douglas L.
January 2004
BMC Genomics;2004, Vol. 5, p1
Academic Journal
Background: While 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. Results: We 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. Conclusion: The methods described have application for functional genomics studies, particularly among non-model organisms.


Related Articles

  • aGEM: an integrative system for analyzing spatial-temporal gene-expression information. Jiménez-Lozano, Natalia; Segura, Joan; Macías, José Ramón; Vega, Juanjo; Carazo, José María // Bioinformatics;Oct2009, Vol. 25 Issue 19, p2566 

    Motivation: The work presented here describes the ‘anatomical Gene-Expression Mapping (aGEM)’ Platform, a development conceived to integrate phenotypic information with the spatial and temporal distributions of genes expressed in the mouse. The aGEM Platform has been built by...

  • c hip a rtifact CORRECT ion (caCORRECT): A Bioinformatics System for Quality Assurance of Genomics and Proteomics Array Data. Todd Stokes; Richard Moffitt; John Phan; May Wang // Annals of Biomedical Engineering;Jun2007, Vol. 35 Issue 6, p1068 

    Abstract  Quality assurance of high throughput “-omics” data is a major concern for biomedical discovery and translational medicine, and is considered a top priority in bioinformatics and systems biology. Here, we report a web-based bioinformatics tool...

  • Assessing the functional structure of genomic data. C. Huttenhower; O.G. Troyanskaya // Bioinformatics;Jul2008, Vol. 24 Issue 13, pi330 

    Motivation: The availability of genome-scale data has enabled an abundance of novel analysis techniques for investigating a variety of systems-level biological relationships. As thousands of such datasets become available, they provide an opportunity to study high-level associations between...

  • Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements. Mieczkowski, Jakub; Tyburczy, Magdalena E.; Dabrowski, Michal; Pokarowski, Piotr // BMC Bioinformatics;2010, Vol. 11, p104 

    Background: Affymetrix GeneChip microarrays are popular platforms for expression profiling in two types of studies: detection of differential expression computed by p-values of t-test and estimation of fold change between analyzed groups. There are many different preprocessing algorithms for...

  • Genomic and physiological responses to strong selective pressure during late organogenesis: few gene expression changes found despite striking morphological differences. Bozinovic, Goran; Sit, Tim L.; Giulio, Richard Di; Wills, Lauren F.; Oleksiak, Marjorie F. // BMC Genomics;2013, Vol. 14 Issue 1, p1 

    Background Adaptations to a new environment, such as a polluted one, often involve large modifications of the existing phenotypes. Changes in gene expression and regulation during critical developmental stages may explain these phenotypic changes. Embryos from a population of the teleost fish,...

  • A quantization method based on threshold optimization for microarray short time series. Camillo, Barbara Di; Sanchez-Cabo, Fatima; Toffolo, Gianna; Nair, Sreekumaran K; Trajanoski, Zlatko; Cobelli, Claudio // BMC Bioinformatics;2005 Supplement 4, Vol. 6, pS11 

    Background: Reconstructing regulatory networks from gene expression problem of functional genomics. In microarray studies the number of compared to the number of genes, thus the use of discrete data may of finding random associations between genes. Results: A quantization method, based on a...

  • Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks. Chang H. Seo; Jeong-Rae Kim; Man-Sun Kim; Kwang-Hyun Cho // Bioinformatics;Aug2009, Vol. 25 Issue 15, p1898 

    Motivation: Spatio-temporal regulation of gene expression is an indispensable characteristic in the development processes of all animals. ‘Master switches’, a central set of regulatory genes whose states (on/off or activated/deactivated) determine specific developmental fate or...

  • Effect of CAR activation on selected metabolic pathways in normal and hyperlipidemic mouse livers. Režen, Tadeja; Tamasi, Viola; Lövgren-Sandblom, Anita; Björkhem, Ingemar; Meyer, Urs A.; Rozman, Damjana // BMC Genomics;2009, Vol. 10, p384 

    Background: The declining cost of DNA sequencing is making genome sequencing a feasible option for more organisms, including many of interest to ecologists and evolutionary biologists. While obtaining high-depth, completely assembled genome sequences for most non-model organisms remains...

  • Functional Genomics of Physiological Plasticity and Local Adaptation in Killifish. Whitehead, Andrew; Galvez, Fernando; Zhang, Shujun; Williams, Larissa M.; Oleksiak, Marjorie F. // Journal of Heredity;Sep2011, Vol. 102 Issue 5, p499 

    Evolutionary solutions to the physiological challenges of life in highly variable habitats can span the continuum from evolution of a cosmopolitan plastic phenotype to the evolution of locally adapted phenotypes. Killifish (Fundulus sp.) have evolved both highly plastic and locally adapted...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics