Mfuzz: A software package for soft clustering of microarray data

Kumar, Lokesh; Futschik, Matthias E.

doi:10.6026/97320630002005

Cited by 1,242 publications

(1,006 citation statements)

References 6 publications

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“…The remaining root-expressed genes' expression profiles were standardized such that mean = 0 and SD = 1, followed by fuzzy C-means clustering using R package Mfuzz (Kumar and E Futschik, 2007). After monitoring the minimum distances between cluster centroids, the number of groups was optimized as 9.…”

Section: Gene Expression Pattern Type Assignmentmentioning

confidence: 99%

“…Expression profile types were then assigned by clustering using the Mfuzz program (Kumar and E Futschik, 2007) as above or by FC (described below). Comparisons within species for the same expression profile types were assigned a P value of 0, whereas comparisons within species for different expression profile types were assigned a P value of 1 because each species was only able to have one expression profile type within a given family in this analysis.…”

Section: Generation and Analyses Of Supergenesmentioning

confidence: 99%

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Conserved Gene Expression Programs in Developing Roots from Diverse Plants

Huang

Schiefelbein

2015

The Plant Cell

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The molecular basis for the origin and diversification of morphological adaptations is a central issue in evolutionary developmental biology. Here, we defined temporal transcript accumulation in developing roots from seven vascular plants, permitting a genome-wide comparative analysis of the molecular programs used by a single organ across diverse species. The resulting gene expression maps uncover significant similarity in the genes employed in roots and their developmental expression profiles. The detailed analysis of a subset of 133 genes known to be associated with root development in Arabidopsis thaliana indicates that most of these are used in all plant species. Strikingly, this was also true for root development in a lycophyte (Selaginella moellendorffii), which forms morphologically different roots and is thought to have evolved roots independently. Thus, despite vast differences in size and anatomy of roots from diverse plants, the basic molecular mechanisms employed during root formation appear to be conserved. This suggests that roots evolved in the two major vascular plant lineages either by parallel recruitment of largely the same developmental program or by elaboration of an existing root program in the common ancestor of vascular plants.

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Section: Gene Expression Pattern Type Assignmentmentioning

confidence: 99%

Section: Generation and Analyses Of Supergenesmentioning

confidence: 99%

Conserved Gene Expression Programs in Developing Roots from Diverse Plants

Huang

Schiefelbein

2015

The Plant Cell

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“…83 Loci were required to have at least one read associated per stage, a between-stage variance of at least two and an associated target outside of any piRNA cluster, leaving 7,351 loci. Read count data were similarly normalized and standardized as described above.…”

Section: Enrichment Of Individual Pirnas In Temporal Profilesmentioning

confidence: 99%

Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis

et al. 2017

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PIWI-interacting RNAs (piRNAs) and associated proteins comprise a conserved pathway for silencing transposons in metazoan germlines. piRNA pathway components are also expressed in multipotent somatic stem cells in various organisms. piRNA functions have been extensively explored in bilaterian model systems, however, comprehensive studies in non-bilaterian phyla remain limited. Here we investigate the piRNA pathway during the development of Nematostella vectensis, a well-established model system belonging to Cnidaria, the sister group to Bilateria. To date, no population of somatic stem cells has been identified in this organism, despite its long life-span and regenerative capacities that require a constant cell-renewal. We show that Nematostella piRNA pathway components are broadly expressed in early developmental stages, while piRNAs themselves show differential expression, suggesting specific developmental roles of distinct piRNA families. In adults, piRNA associated proteins are enriched in the germline but also expressed in somatic cells, indicating putative stem cell properties. Furthermore, we provide experimental evidence that Nematostella piRNAs cleave transposable elements as well as protein-coding genes. Our results demonstrate that somatic expression of piRNA associated proteins as well as the roles of piRNAs in transposon repression and gene regulation are likely ancestral features that evolved before the split between Cnidaria and Bilateria.

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“…We found 510 genes that were differentially expressed. They were sorted into six different groups according to their expression profile using the c-means algorithm (Kumar and Futschik, 2007) (Supplementary Figure S3), and putative biological functions were assigned based on clusters of orthologous groups (Supplementary Figure S4). Several microarray data were confirmed by quantitative RT-PCR (Supplementary Table S3).…”

Section: Cultivation Mediummentioning

confidence: 99%

Cross-feeding and interkingdom communication in dual-species biofilms of Streptococcus mutans and Candida albicans

et al. 2014

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Polymicrobial biofilms are of large medical importance, but relatively little is known about the role of interspecies interactions for their physiology and virulence. Here, we studied two human pathogens co-occuring in the oral cavity, the opportunistic fungus Candida albicans and the caries-promoting bacterium Streptococcus mutans. Dual-species biofilms reached higher biomass and cell numbers than mono-species biofilms, and the production of extracellular polymeric substances (EPSs) by S. mutans was strongly suppressed, which was confirmed by scanning electron microscopy, gas chromatography-mass spectrometry and transcriptome analysis. To detect interkingdom communication, C. albicans was co-cultivated with a strain of S. mutans carrying a transcriptional fusion between a green fluorescent protein-encoding gene and the promoter for sigX, the alternative sigma factor of S. mutans, which is induced by quorum sensing signals. Strong induction of sigX was observed in dual-species biofilms, but not in single-species biofilms. Conditioned media from mixed biofilms but not from C. albicans or S. mutans cultivated alone activated sigX in the reporter strain. Deletion of comS encoding the synthesis of the sigX-inducing peptide precursor abolished this activity, whereas deletion of comC encoding the competence-stimulating peptide precursor had no effect. Transcriptome analysis of S. mutans confirmed induction of comS, sigX, bacteriocins and the downstream late competence genes, including fratricins, in dual-species biofilms. We show here for the first time the stimulation of the complete quorum sensing system of S. mutans by a species from another kingdom, namely the fungus C. albicans, resulting in fundamentally changed virulence properties of the caries pathogen.

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Mfuzz: A software package for soft clustering of microarray data

Cited by 1,242 publications

References 6 publications

Conserved Gene Expression Programs in Developing Roots from Diverse Plants

Conserved Gene Expression Programs in Developing Roots from Diverse Plants

Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis

Cross-feeding and interkingdom communication in dual-species biofilms of Streptococcus mutans and Candida albicans

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