Visualization of Intersecting Groups Based on Hypergraphs

Santamaría, Rodrigo; Therón, Roberto

doi:10.1587/transinf.e93.d.1957

Cited by 8 publications

(3 citation statements)

References 28 publications

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“…Hub genes were identified using VENN analysis of time-dependent DEGs and module genes using the UpSetR (version 1.4.0) package [27] in R.…”

Section: Identification Of Hub Genes Whose Expression Changed Over Ti...mentioning

confidence: 99%

Time-series analysis of hematopoietic stem cells

Han,

Duan,

et al. 2024

Medicine

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This study aimed to investigate the molecular mechanisms underlying the aging of hematopoietic stem cells (HSCs). Gene expression profile GSE32719 was downloaded from the Gene Expression Omnibus database, including 14 young, 5 middle, and 8 old HSCs. Differential expression analysis, short time-series expression miner analysis, and weighted co-expression network analysis were conducted to screen for hub genes whose expression changed over time during HSC aging. Subsequently, functional enrichment and multiple regulatory network analyses of the hub genes were performed. A total of 124 intersecting time-dependent differentially expressed and module genes were obtained, which were considered hub genes whose expression changed over time during HSC aging. Hub genes were significantly enriched in pathways such as the Hippo and AMP-activated protein kinase (AMPK) signaling pathways. Moreover, AP-1 Transcription Factor Subunit (FOS) and sirtuin 1 (SIRT1) had higher degrees in the protein-protein interaction network, were regulated by more transcription factors (TFs), such as Sp1 transcription factor (SP1) and BRCA1 DNA repair-associated (BRCA1), in the TF-mRNA-miRNA network, were associated with more diseases in the disease-gene network, and could be targeted by more drugs in the drug-gene network. Furthermore, SIRT1 was targeted by miR-9-5p in the TF-mRNA-miRNA network. Hub genes such as FOS and SIRT1 and key pathways such as the Hippo and AMPK signaling pathways may play crucial roles in HSC aging. Moreover, FOS and SIRT1 were regulated by SP1 and BRCA1, respectively, during HSC aging. Furthermore, miR-9-5p may modulate HSC aging by targeting SIRT1. Thus, FOS and SIRT1 may be potential therapeutic targets for age-related hematopoietic dysfunction.

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“…Hub genes were identified using VENN analysis of time-dependent DEGs and module genes using the UpSetR (version 1.4.0) package [27] in R.…”

Section: Identification Of Hub Genes Whose Expression Changed Over Ti...mentioning

confidence: 99%

Time-series analysis of hematopoietic stem cells

Han,

Duan,

et al. 2024

Medicine

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“…The number of elements and sets influences the effectiveness of a visualization. For many elements and groups, augmenting a contour‐based visualization is a possibility [ST10], or a highly‐interactive analysis environment is a necessity [FMH08].…”

Section: Related Workmentioning

confidence: 99%

Kelp Diagrams: Point Set Membership Visualization

Dinkla

Kreveld

Speckmann

et al. 2012

Computer Graphics Forum

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Figure 1: Kelp Diagrams applied to a metabolic network (left) and cities on a map (right). AbstractWe present Kelp Diagrams, a novel method to depict set relations over points, i.e., elements with predefined positions. Our method creates schematic drawings and has been designed to take aesthetic quality, efficiency, and effectiveness into account. This is achieved by a routing algorithm, which links elements that are part of the same set by constructing minimum cost paths over a tangent visibility graph. There are two styles of Kelp Diagrams to depict overlapping sets, a nested and a striped style, each with its own strengths and weaknesses. We compare Kelp Diagrams with two existing methods and show that our approach provides a more consistent and clear depiction of both element locations and their set relations.

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“…Una de estas soluciones es la definición de agrupamientos o clusters, que consiste en colocar diversos elementos relacionados en una agrupación, lo que evita el uso de aristas para indicar relaciones [13,228,206]. Para el caso específico de la visualización de ontologías, el uso de una solución basada en agrupaciones, generaría una visualización con intersecciones entre estas, como se describe en [232].…”

Section: Problemática Visual De Las Herramientasunclassified

Analítica visual aplicada a la Ingeniería de Ontologías

Navarro¹

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Los resultados de las evaluaciones han indicado, por un lado, que los procesos, los flujos de trabajo y las tareas definidas, son coherentes con los objetivos definidos. Este resultado se debe en gran parte a que estas tareas se han adaptado a partir de metodologías previamente definidas. Por otro lado, la evaluación de funcionalidad en el caso de estudio, ha permitido detectar algunos aspectos mejorables, así como también ha servido para la validación general de la herramienta y las diversas técnicas de visualización e interacción implementadas en ella.

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Visualization of Intersecting Groups Based on Hypergraphs

Cited by 8 publications

References 28 publications

Time-series analysis of hematopoietic stem cells

Time-series analysis of hematopoietic stem cells

Kelp Diagrams: Point Set Membership Visualization

Analítica visual aplicada a la Ingeniería de Ontologías

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