FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments

Al‐Shahrour, Fátima; Mínguez, Pablo; Tárraga, Joaquín; Medina, Ignacio; Alloza, Eva; Montaner, David; Dopazo, Joaquı́n

doi:10.1093/nar/gkm260

Cited by 234 publications

(216 citation statements)

References 42 publications

(50 reference statements)

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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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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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“…We used program search parameters Blastx (BLAST program), nr (Blast database), retrieve 10 Blast hits and Blast expectation ¼ 10 23 default value. A Fisher's exact test in the FATIGO [29] package that is integrated within BLAST2GO was used to test for significant annotation differences between two sets of loci (i.e. a group of putative candidate loci and the reference set of all loci that were annotated).…”

Section: (B) Bioinformaticsmentioning

confidence: 99%

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

et al. 2016

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Migration traits are presumed to be complex and to involve interaction among multiple genes. We used both univariate analyses and a multivariate random forest (RF) machine learning algorithm to conduct association mapping of 15 239 single nucleotide polymorphisms (SNPs) for adult migration-timing phenotype in steelhead (Oncorhynchus mykiss). Our study focused on a model natural population of steelhead that exhibits two distinct migration-timing life histories with high levels of admixture in nature. Neutral divergence was limited between fish exhibiting summer-and winter-run migration owing to high levels of interbreeding, but a univariate mixed linear model found three SNPs from a major effect gene to be significantly associated with migration timing ( p , 0.000005) that explained 46% of trait variation. Alignment to the annotated Salmo salar genome provided evidence that all three SNPs localize within a 46 kb region overlapping GREB1-like (an oestrogen target gene) on chromosome Ssa03. Additionally, multivariate analyses with RF identified that these three SNPs plus 15 additional SNPs explained up to 60% of trait variation. These candidate SNPs may provide the ability to predict adult migration timing of steelhead to facilitate conservation management of this species, and this study demonstrates the benefit of multivariate analyses for association studies.

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“…The identified proteins were analyzed using Ingenuity Pathways Analysis (Ingenuityா Systems). Functional analysis was performed using the FatiGOϩ functional annotation software in the Babelomics suite (22,23). The fraction of proteins identified out of those present in thymocytes was estimated from the set of curated mouse thymus ESTs.…”

Section: Methodsmentioning

confidence: 99%

“…Functional annotations of the proteins identified in the two experiments were compared using the FatiGOϩ algorithm (22,23). Proteins that had been identified and quantified in the wild type or p53 K317R experiments were classified by their Gene Ontology (GO) molecular function, level 3 (supplemental Fig.…”

Section: Proteomics Analysis Of the Wild Type And P53mentioning

confidence: 99%

Quantitative Proteomics Analysis of the Effects of Ionizing Radiation in Wild Type and p53K317R Knock-in Mouse Thymocytes

Jenkins

Mazur

Rossi

et al. 2008

Molecular & Cellular Proteomics

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The tumor suppressor protein p53 is a sequence-specific transcription factor that has crucial roles in apoptosis, cell cycle arrest, cellular senescence, and DNA repair. Following exposure to a variety of stresses, p53 becomes posttranslationally modified with concomitant increases in activity and stability. To better understand the role of acetylation of Lys-317 in mouse p53, the effect of ionizing radiation (IR) on the thymocytes of p53 K317R knock-in mice was studied at the global level. Using cleavable ICAT quantitative mass spectrometry, the effect of IR on protein levels in either the wild type or p53 K317R thymocytes was determined. We found 102 proteins to be significantly affected by IR in the wild type thymocytes, including several whose expression has been shown to be directly regulated by p53. When the effects of IR in the wild type and p53 K317R samples were compared, 46 proteins were found to be differently affected (p < 0.05). The p53 K317R mutation has widespread effects on specific protein levels following IR, including the levels of proteins involved in apoptosis, transcription, and translation. Pathway analysis of the differently regulated proteins suggests an increase in p53 activity in the p53 K317R thymocytes as well as a decrease in tumor necrosis factor ␣ signaling. These results suggest that acetylation of Lys-317 modulates the functions of p53 and influences the cross-talk between

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FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments

Cited by 234 publications

References 42 publications

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

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

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

Quantitative Proteomics Analysis of the Effects of Ionizing Radiation in Wild Type and p53K317R Knock-in Mouse Thymocytes

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