Logical Development of the Cell Ontology

Meehan, Terrence F.; Masci, Anna Maria; Abdulla, Amina; Cowell, Lindsay G.; Blake, Judith A.; Mungall, Christopher J.; Diehl, Alexander D.

doi:10.1186/1471-2105-12-6

Cited by 123 publications

(124 citation statements)

References 32 publications

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“…We then calculated the statistical significance of expression enrichment or depletion of each miRNA (Table S13) with respect to cell ontology clusters (Table S14) defined by the FANTOM5 cell ontology annotation 30,31 , which organizes FANTOM5 samples by cell type in a hierarchical framework. Of miRNAs in the robust set, 54% had enriched expression in their statistically most significant cell ontology cluster, whereas 27% were broadly expressed, with depleted expression in their statistically most significant cell ontology cluster.…”

Section: Resultsmentioning

confidence: 99%

“…We used the FANTOM5 cell ontology 30,31 to create cell ontology clusters (Tables S14 and S20). We performed a likelihood-ratio test comparing the expression data between the samples in each cell ontology cluster and the background, consisting of all other samples listed in Tables S14 and S20, modeling the tag counts by a negative binomial distribution.…”

Section: Cell Type Specificity Indexmentioning

confidence: 99%

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An integrated expression atlas of miRNAs and their promoters in human and mouse

Rie¹,

Abugessaisa²,

et al. 2017

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MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.

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Section: Resultsmentioning

confidence: 99%

Section: Cell Type Specificity Indexmentioning

confidence: 99%

An integrated expression atlas of miRNAs and their promoters in human and mouse

Rie¹,

Abugessaisa²,

et al. 2017

Self Cite

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“…1a; see the full sample list in Supplementary Table 1). To facilitate data mining all samples were annotated using structured ontologies (Cell Ontology 7 , Uberon 8 , Disease Ontology 9 ). The results of all analyses are summarized in the FANTOM5 online resource (http://fantom.gsc.riken.jp/5).…”

Section: The Fantom5 Promoter Atlasmentioning

confidence: 99%

A promoter-level mammalian expression atlas

Forrest¹,

Kawaji²,

Rehli³

et al. 2014

Nature

1,802

1,597

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Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

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“…the January 2013 version of CellType ontology [19,20] (available via http://bioportal.bioontology.org) does not yet support the functionally critical distinction [21] between dermal fibroblasts of papillary and reticular origin);…”

Section: Discussionmentioning

confidence: 99%

Functional tissue units and their primary tissue motifs in multi-scale physiology

et al. 2013

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BackgroundHistology information management relies on complex knowledge derived from morphological tissue analyses. These approaches have not significantly facilitated the general integration of tissue- and molecular-level knowledge across the board in support of a systematic classification of tissue function, as well as the coherent multi-scale study of physiology. Our work aims to support directly these integrative goals.ResultsWe describe, for the first time, the precise biophysical and topological characteristics of functional units of tissue. Such a unit consists of a three-dimensional block of cells centred around a capillary, such that each cell in this block is within diffusion distance from any other cell in the same block. We refer to this block as a functional tissue unit. As a means of simplifying the knowledge representation of this unit, and rendering this knowledge more amenable to automated reasoning and classification, we developed a simple descriptor of its cellular content and anatomical location, which we refer to as a primary tissue motif. In particular, a primary motif captures the set of cellular participants of diffusion-mediated interactions brokered by secreted products to create a tissue-level molecular network.ConclusionsMulti-organ communication, therefore, may be interpreted in terms of interactions between molecular networks housed by interconnected functional tissue units. By extension, a functional picture of an organ, or its tissue components, may be rationally assembled using a collection of these functional tissue units as building blocks. In our work, we outline the biophysical rationale for a rigorous definition of a unit of functional tissue organization, and demonstrate the application of primary motifs in tissue classification. In so doing, we acknowledge (i) the fundamental role of capillaries in directing and radically informing tissue architecture, as well as (ii) the importance of taking into full account the critical influence of neighbouring cellular environments when studying complex developmental and pathological phenomena.

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Logical Development of the Cell Ontology

Cited by 123 publications

References 32 publications

An integrated expression atlas of miRNAs and their promoters in human and mouse

An integrated expression atlas of miRNAs and their promoters in human and mouse

A promoter-level mammalian expression atlas

Functional tissue units and their primary tissue motifs in multi-scale physiology

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