Network propagation in the cytoscape cyberinfrastructure

Carlin, Daniel E.; Demchak, Barry; Pratt, Dexter; Sage, Eric; Ideker, Trey

doi:10.1371/journal.pcbi.1005598

Cited by 76 publications

(64 citation statements)

References 20 publications

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“…The largest difference in connectivity was found in a E3 ubiquitin ligase gene family shown to play a role in ABA signaling, with the Arabidopsis homolog known as ring finger of seed longevity1 (RSL1). To explore differences in network connections of RSL1 between the two species, we employed the diffusion algorithm (Carlin et al, 2017) in Cytoscape which finds strongly interactive nodes to a target of interest. For both species, we found the diffusion network for the RSL1 gene.…”

Section: Methodsmentioning

confidence: 99%

Altered Gene Regulatory Networks are Associated with the Transition from C₃ to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)

Heyduk¹,

Hwang²,

Silvera

et al. 2018

Preprint

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Crassulacean acid metabolism (CAM) photosynthesis is a modification of the core C3 photosynthetic pathway that improves the ability of plants to assimilate carbon in water-limited environments. CAM plants fix CO2 mostly at night, when transpiration rates are low. All of the CAM pathway genes exist in ancestral C3 species, but the timing and magnitude of expression are greatly altered between C3 and CAM species. Understanding these regulatory changes is key to elucidating the mechanism by which CAM evolved from C3. Here we use two closely related species in the Orchidaceae, Erycina pusilla (CAM) and Erycina crista-galli (C3), to conduct comparative transcriptomic analyses across multiple time points. Clustering of genes with expression variation across the diel cycle revealed some canonical CAM pathway genes similarly expressed in both species, regardless of photosynthetic pathway. However, gene network construction indicated that 149 gene families had significant differences in network connectivity and were further explored for these functional enrichments. Genes involved in light sensing and ABA signaling were some of the most differently connected genes between the C3 and CAM Erycina species, in agreement with the contrasting diel patterns of stomatal conductance in C3 and CAM plants. Our results suggest changes to transcriptional cascades are important for the transition from C3 to CAM photosynthesis in Erycina.

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Section: Methodsmentioning

confidence: 99%

Altered Gene Regulatory Networks are Associated with the Transition from C₃ to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)

Heyduk¹,

Hwang²,

Silvera

et al. 2018

Preprint

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“…The networks were built starting from a list of seed nodes-all genes included in build 1 of Cel-lAge, part of the Human Ageing Genomic Resources [28]. Network propagation was measured using the Cytoscape plugin Diffusion [106].…”

Section: Networkmentioning

confidence: 99%

A multidimensional systems biology analysis of cellular senescence in aging and disease

et al. 2020

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Background: Cellular senescence, a permanent state of replicative arrest in otherwise proliferating cells, is a hallmark of aging and has been linked to aging-related diseases. Many genes play a role in cellular senescence, yet a comprehensive understanding of its pathways is still lacking. Results: We develop CellAge (http://genomics.senescence.info/cells), a manually curated database of 279 human genes driving cellular senescence, and perform various integrative analyses. Genes inducing cellular senescence tend to be overexpressed with age in human tissues and are significantly overrepresented in anti-longevity and tumor-suppressor genes, while genes inhibiting cellular senescence overlap with pro-longevity and oncogenes. Furthermore, cellular senescence genes are strongly conserved in mammals but not in invertebrates. We also build cellular senescence protein-protein interaction and co-expression networks. Clusters in the networks are enriched for cell cycle and immunological processes. Network topological parameters also reveal novel potential cellular senescence regulators. Using siRNAs, we observe that all 26 candidates tested induce at least one marker of senescence with 13 genes (C9orf40, CDC25A, CDCA4, CKAP2, GTF3C4, HAUS4, IMMT, MCM7, MTHFD2, MYBL2, NEK2, NIPA2, and TCEB3) decreasing cell number, activating p16/p21, and undergoing morphological changes that resemble cellular senescence. Conclusions: Overall, our work provides a benchmark resource for researchers to study cellular senescence, and our systems biology analyses reveal new insights and gene regulators of cellular senescence.

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“…Resources (Tacutu et al, 2018). Network propagation was measured using the Cytoscape plugin Diffusion (Carlin et al, 2017).…”

Section: Networkmentioning

confidence: 99%

A Multidimensional Systems Biology Analysis of Cellular Senescence in Ageing and Disease

Avelar

Ortega

Tăcutu

et al. 2019

Preprint

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Cellular senescence, a permanent state of replicative arrest in otherwise proliferating cells, is a hallmark of ageing and has been linked to ageing-related diseases like cancer. Senescent cells have been shown to accumulate in tissues of aged organisms which in turn can lead to chronic inflammation. Many genes have been associated with cell senescence, yet a comprehensive understanding of cell senescence pathways is still lacking. To this end, we created CellAge (http://genomics.senescence.info/cells), a manually curated database of 279 human genes associated with cellular senescence, and performed various integrative and functional analyses. We observed that genes promoting cell senescence tend to be overexpressed with age in human tissues and are also significantly overrepresented in anti-longevity and tumour-suppressor gene databases.By contrast, genes inhibiting cell senescence overlapped with pro-longevity genes and oncogenes.Furthermore, an evolutionary analysis revealed a strong conservation of senescence-associated genes in mammals, but not in invertebrates. Using the CellAge genes as seed nodes, we also built protein-protein interaction and co-expression networks. Clusters in the networks were enriched for cell cycle and immunological processes. Network topological parameters also revealed novel potential senescence-associated regulators. We then used siRNAs and observed that of 26 candidates tested, 19 induced markers of senescence. Overall, our work provides a new resource for researchers to study cell senescence and our systems biology analyses provide new insights and novel genes regarding cell senescence.

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Network propagation in the cytoscape cyberinfrastructure

Cited by 76 publications

References 20 publications

Altered Gene Regulatory Networks are Associated with the Transition from C₃ to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)

Altered Gene Regulatory Networks are Associated with the Transition from C₃ to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)

A multidimensional systems biology analysis of cellular senescence in aging and disease

A Multidimensional Systems Biology Analysis of Cellular Senescence in Ageing and Disease

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Network propagation in the cytoscape cyberinfrastructure

Cited by 76 publications

References 20 publications

Altered Gene Regulatory Networks are Associated with the Transition from C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)

Altered Gene Regulatory Networks are Associated with the Transition from C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)

A multidimensional systems biology analysis of cellular senescence in aging and disease

A Multidimensional Systems Biology Analysis of Cellular Senescence in Ageing and Disease

Contact Info

Product

Resources

About

Altered Gene Regulatory Networks are Associated with the Transition from C₃ to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)

Altered Gene Regulatory Networks are Associated with the Transition from C₃ to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)