Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

Medina, Ignacio; Carbonell, José; Pulido, Luis; Madeira, Sara C.; Goetz, Stefan M.; Conesa, Ana; Tárraga, Joaquín; Pascual-Montano, Alberto; Nogales-Cadenas, Rubén; Santoyo, Javier; Garcı́a, Francisco; Marbà, Martina; Montaner, David; Dopazo, Joaquı́n

doi:10.1093/nar/gkq388

Cited by 291 publications

(283 citation statements)

References 35 publications

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“…Additional normalization (within and between microarrays) was applied to the experiments using the Babelomics 4 gene expression suite 17 . The resulting box-plots of the normalized expression ratios showed similar log-ratio value distribution within and between the arrays (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum

et al. 2014

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The Dead Sea is one of the most hypersaline habitats on Earth. The fungus Eurotium rubrum (Eurotiomycetes) is among the few species able to survive there. Here we highlight its adaptive strategies, based on genome analysis and transcriptome profiling. The 26.2 Mb genome of E. rubrum shows, for example, gains in gene families related to stress response and losses with regard to transport processes. Transcriptome analyses under different salt growth conditions revealed, among other things differentially expressed genes encoding ion and metabolite transporters. Our findings suggest that long-term adaptation to salinity requires cellular and metabolic responses that differ from short-term osmotic stress signalling. The transcriptional response indicates that halophilic E. rubrum actively counteracts the salinity stress. Many of its genes encode for proteins with a significantly higher proportion of acidic amino acid residues. This trait is characteristic of the halophilic prokaryotes as well, supporting the theory of convergent evolution under extreme hypersaline stress.

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Section: Resultsmentioning

confidence: 99%

Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum

et al. 2014

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“…We ranked all genes on the basis of raw P value. Ranked lists were assessed for Gene Ontology enrichment, using the logistic regression function in Babelomics 4.3 (73). This threshold-free analysis determines Gene Ontology categories that are represented by genes near the top of a ranked list (10).…”

Section: Methodsmentioning

confidence: 99%

“…We used mouse GO annotations curated by the database Babelomics 4.3 (73). For stickleback and honey bee, we derived Gene Ontology assignments, using protein family annotations from the database PANTHER (76).…”

Section: Methodsmentioning

confidence: 99%

Neuromolecular responses to social challenge: Common mechanisms across mouse, stickleback fish, and honey bee

Rittschof

Bukhari

Sloofman

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

141

196

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Certain complex phenotypes appear repeatedly across diverse species due to processes of evolutionary conservation and convergence. In some contexts like developmental body patterning, there is increased appreciation that common molecular mechanisms underlie common phenotypes; these molecular mechanisms include highly conserved genes and networks that may be modified by lineage-specific mutations. However, the existence of deeply conserved mechanisms for social behaviors has not yet been demonstrated. We used a comparative genomics approach to determine whether shared neuromolecular mechanisms could underlie behavioral response to territory intrusion across species spanning a broad phylogenetic range: house mouse (Mus musculus), stickleback fish (Gasterosteus aculeatus), and honey bee (Apis mellifera). Territory intrusion modulated similar brain functional processes in each species, including those associated with hormone-mediated signal transduction and neurodevelopment. Changes in chromosome organization and energy metabolism appear to be core, conserved processes involved in the response to territory intrusion. We also found that several homologous transcription factors that are typically associated with neural development were modulated across all three species, suggesting that shared neuronal effects may involve transcriptional cascades of evolutionarily conserved genes. Furthermore, immunohistochemical analyses of a subset of these transcription factors in mouse again implicated modulation of energy metabolism in the behavioral response. These results provide support for conserved genetic "toolkits" that are used in independent evolutions of the response to social challenge in diverse taxa.genetic hotspot | NF-κB signaling | brain metabolism | aggression S imilar phenotypes can have a shared molecular basis, even among distantly related species (1-3). This phenomenon has been observed for an array of traits, including morphological adaptations like coat color or wing patterning, rapid adaptations like drug resistance, and artificially selected phenological traits like flowering time (reviewed in ref. 2). Shared molecular mechanisms can arise convergently as a result of de novo mutations at genetic hotspots (2) or as a result of conservation. Both of these processes result in "genetic toolkits" or genes that are repeatedly used over evolutionary time to give rise to similar phenotypes (3). The phenomenon of genetic toolkits challenges fundamental notions about evolutionary convergence, conservation, and the origins of biodiversity.The role of genetic toolkits in shaping behavioral phenotypes is unclear (4, 5). Behaviors are typically polygenic (6) and they show great nuance and plasticity within a species, raising the possibility that cross-species similarities in behavior are superficial. Social behaviors in particular present a challenge to the genetic toolkit concept: these behaviors are critical to survival and reproductive success, but across species there is significant variation in the contexts for an...

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“…Fisher's exact test as implemented in Blast2GO was used to compute the enrichment P ‐value for each GO term. Enrichment analyses were also performed on identified Pfam domains using F atiscan at P‐ value < 0.05 (Al‐Shahrour et al ., 2007; Medina et al ., 2010). …”

Section: Methodsmentioning

confidence: 99%

Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce

et al. 2015

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Summary Association studies are widely utilized to analyze complex traits but their ability to disclose genetic architectures is often limited by statistical constraints, and functional insights are usually minimal in nonmodel organisms like forest trees.We developed an approach to integrate association mapping results with co‐expression networks. We tested single nucleotide polymorphisms (SNPs) in 2652 candidate genes for statistical associations with wood density, stiffness, microfibril angle and ring width in a population of 1694 white spruce trees (Picea glauca).Associations mapping identified 229–292 genes per wood trait using a statistical significance level of P < 0.05 to maximize discovery. Over‐representation of genes associated for nearly all traits was found in a xylem preferential co‐expression group developed in independent experiments. A xylem co‐expression network was reconstructed with 180 wood associated genes and several known MYB and NAC regulators were identified as network hubs. The network revealed a link between the gene PgNAC8, wood stiffness and microfibril angle, as well as considerable within‐season variation for both genetic control of wood traits and gene expression. Trait associations were distributed throughout the network suggesting complex interactions and pleiotropic effects.Our findings indicate that integration of association mapping and co‐expression networks enhances our understanding of complex wood traits.

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Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

Cited by 291 publications

References 35 publications

Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum

Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum

Neuromolecular responses to social challenge: Common mechanisms across mouse, stickleback fish, and honey bee

Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce

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