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Gimaret-Carpentier, Clémentine; Chessel, Daniel; Pascal, Jean‐Pierre

doi:10.1023/a:1009708824434

Cited by 27 publications

(5 citation statements)

References 41 publications

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“…CIA starts by performing a multivariate analysis like principal component analysis (PCA) [41], non-symmetrical correspondence analysis (NSC) [42] or correspondence analysis (CA) [43] on each individual data set. The produced results are a set of principal axes that maximize the projected variability (inertia) of each data set independently.…”

Section: Methodsmentioning

confidence: 99%

Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data

2014

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BackgroundTechnological improvements have shifted the focus from data generation to data analysis. The availability of large amounts of data from transcriptomics, protemics and metabolomics experiments raise new questions concerning suitable integrative analysis methods. We compare three integrative analysis techniques (co-inertia analysis, generalized singular value decomposition and integrative biclustering) by applying them to gene and protein abundance data from the six life cycle stages of Plasmodium falciparum. Co-inertia analysis is an analysis method used to visualize and explore gene and protein data. The generalized singular value decomposition has shown its potential in the analysis of two transcriptome data sets. Integrative Biclustering applies biclustering to gene and protein data.ResultsUsing CIA, we visualize the six life cycle stages of Plasmodium falciparum, as well as GO terms in a 2D plane and interpret the spatial configuration. With GSVD, we decompose the transcriptomic and proteomic data sets into matrices with biologically meaningful interpretations and explore the processes captured by the data sets. IBC identifies groups of genes, proteins, GO Terms and life cycle stages of Plasmodium falciparum. We show method-specific results as well as a network view of the life cycle stages based on the results common to all three methods. Additionally, by combining the results of the three methods, we create a three-fold validated network of life cycle stage specific GO terms: Sporozoites are associated with transcription and transport; merozoites with entry into host cell as well as biosynthetic and metabolic processes; rings with oxidation-reduction processes; trophozoites with glycolysis and energy production; schizonts with antigenic variation and immune response; gametocyctes with DNA packaging and mitochondrial transport. Furthermore, the network connectivity underlines the separation of the intraerythrocytic cycle from the gametocyte and sporozoite stages.ConclusionUsing integrative analysis techniques, we can integrate knowledge from different levels and obtain a wider view of the system under study. The overlap between method-specific and common results is considerable, even if the basic mathematical assumptions are very different. The three-fold validated network of life cycle stage characteristics of Plasmodium falciparum could identify a large amount of the known associations from literature in only one study.

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Section: Methodsmentioning

confidence: 99%

Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data

2014

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“…obs. ;Daniels, 1992;Gimaret-Carpentier, Dray & Pascal, 2003;Vyas, 2003Vyas, , 2004Davidar, Puyravaud & Leigh, 2005).…”

Section: Sample Numbers and Horizontal Line Between Samples 13 And 14mentioning

confidence: 99%

“…Pronounced climatic gradients are thought to have had a telling impact on the diversity and distribution of Western Ghats organisms, particularly amphibians (e.g. Daniels, 1992;Gadgil, 1996;Gimaret-Carpentier et al, 2003;Davidar et al, 2005), making the biology of I. bombayensis and how it might vary along the Western Ghats an intriguing system worthy of further investigation.…”

Section: Sample Numbers and Horizontal Line Between Samples 13 And 14mentioning

confidence: 99%

Remarkable genetic homogeneity in unstriped, long‐tailed Ichthyophis along 1500 km of the Western Ghats, India

Gower

Dharne

Bhatta³

et al. 2007

Journal of Zoology

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The mountainous Western Ghats are part of a biodiversity hotspot and extend for about 1600 km, lying close and subparallel to the west coast of peninsular India. The region is a centre of diversity for amphibians, and recent preliminary work on some components of both caecilian (Gymnophiona) and frog (Anura) fauna is indicative of a high degree of local endemism. We investigated diversity in mitochondrial rRNA 12S and 16S sequences for long-tailed, unstriped Ichthyophis (Amphibia: Gymnophiona: Ichthyophiidae) that potentially represent four taxonomically confused and poorly known endemic caecilian species. Data were analysed for18 individuals from along c.

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“…In all case studies, matrices L and Q were preliminarily processed by Correspondence Analysis and Fuzzy Correspondence Analysis (Cheveńet et al, 1994) respectively, whereas matrix R was processed either by standardised Principal Component Analysis or Hill and Smith Analysis (Hill and Smith, 1976) depending on the presence of qualitative habitat descriptors next to quantitative ones. Following detrending, residual values in matrix L were rescaled by subtraction to the minimum value of the matrix in order to get null or positive values as negative ones cannot be processed by Correspondence Analysis; this does not affect data structure and relationships between taxa (columns) which are attributed the same importance (same column sum) as in Non-Symmetric Correspondence Analysis (Grimaret-Carpentier et al, 1998). The RLQ-Fourth-corner methodology provides unbiased R-Q correlations unlike the more popular community weighted mean (CWM), which can critically overestimate these correlations as CWM ignores biological variations within communities (Peres-Neto et al, 2017).…”

Section: Trawling-induced Disturbance Gradientmentioning

confidence: 99%

Trawling-induced change in benthic effect trait composition – A multiple case study

Beauchard,

Bradshaw,

Bolam

et al. 2023

Front. Mar. Sci.

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IntroductionThe importance of the response-effect trait dichotomy in marine benthic ecology has garnered recent attention. Response traits, characterising species responses to environmental variations, have been a dominant focus in the development of ecological indicators for ecosystem health assessment. In contrast, effect traits, expressing effects of organism activities on the ecosystem, still do not benefit from an equal interest in spite of the complementary facet that they provide to complete our understanding of functional diversity and ecosystem vulnerability. In this study, we explore the consequences of disturbance by bottom trawl fisheries on benthic effect trait composition.MethodsTo this end, we used different contexts of environmental and trawling conditions from thirteen case studies in European waters and apply the same analytical procedure to derive a gradient that solely account for trawling-induced disturbance (Partial RLQ analysis).ResultsBottom trawling was found to be a selective force of benthic effect trait composition in a majority of case studies. In general, tube-dwelling species were more typical of low trawling frequencies, whereas deep burrowing species were more resistant at high trawling frequencies. Although we report significantly deleterious effects of trawling on benthic ecosystem functions, the effect trait pattern along the gradient was never related to life span, a key response trait generally assumed to express recoverability following disturbance. Furthermore, we show that trends in species multi-functionality and community functional diversity can be negative or positive along the trawling intensity gradient.DiscussionWe discuss the relevance of these results in light of recent developments in the framework of response and effect trait dichotomy, and provide guidelines of trait data analysis in the context of trawl fisheries impact on the sea floor. Our findings emphasize the importance of fundamental concepts from functional ecology in this context and represent a first step toward an assessment of trawling effect more oriented on benthos-mediated biogeochemical processes.

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Untitled

Cited by 27 publications

References 41 publications

Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data

Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data

Remarkable genetic homogeneity in unstriped, long‐tailed Ichthyophis along 1500 km of the Western Ghats, India

Trawling-induced change in benthic effect trait composition – A multiple case study

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