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Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE204711 | GEO | 2022/11/09

REPOSITORIES: GEO

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Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework.

Project description:Advanced computational methods exploit gene expression and epigenetic datasets to predict gene regulatory networks controlled by transcription factors (TFs). These methods have identified cell fate determining TFs but require large amounts of reference data and experimental expertise. Here, we present an easy to use network-based computational framework that exploits enhancers defined by bidirectional transcription, using as sole input CAGE sequencing data to correctly predict TFs key to various human cell types. Next, we applied this Analysis Algorithm for Networks Specified by Enhancers based on CAGE (ANANSE-CAGE) to predict TFs driving red and white blood cell development, and THP-1 leukemia cell immortalization. Further, we predicted TFs that are differentially important to either cell line- or primary- associated MLL-AF9-driven gene programs, and in primary MLL-AF9 acute leukemia. Our approach identified experimentally validated as well as thus far unexplored TFs in these processes. ANANSE-CAGE will be useful to identify transcription factors that are key to any cell fate change using only CAGE-seq data as input.

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Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework [RNAseq_THP1_GSK-LSD1]

Project description:Genome-wide transcription factor binding profiles provide valuable insights into hematopoietic development and malignancies. Today, advanced computational methods exploit cis-regulatory information to predict complex gene regulatory networks controlled by transcription factors. However, these prediction methods still require large amounts of reference data or experimental expertise. Here, we present a low-requirement network-based computational framework that exploits bidirectional transcription marked regulatory elements to identify important transcription factors driving hematopoietic decision making. Using CAGE-seq we predicted TF binding and confirmed experimentally validated TF important in cell conversion strategies by exploiting bidirectional regions. Next, we applied our framework to predict driving transcription factors in induced normal erythropoiesis and early myelopoiesis, as well as in acute myeloid leukemia associated MLL-AF9-driven immortalisation. Our approach allowed the identification of experimentally validated as well as thus far unexplored transcription factors in these processes.

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Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework [CAGEseq_THP1_GSK-LSD1]

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Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework [CAGEseq_MLLAF9-AML]

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Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework

Project description:Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework

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Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework [CAGEseq_THP1_GSK-LSD1]

Project description:Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework [CAGEseq_THP1_GSK-LSD1]

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Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework [RNAseq_THP1_GSK-LSD1]

Project description:Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework [RNAseq_THP1_GSK-LSD1]

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Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework [CAGEseq_MLLAF9-AML]

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Assessing Computational Model Credibility Using a Risk-Based Framework: Application to Hemolysis in Centrifugal Blood Pumps.

Project description:Medical device manufacturers using computational modeling to support their device designs have traditionally been guided by internally developed modeling best practices. A lack of consensus on the evidentiary bar for model validation has hindered broader acceptance, particularly in regulatory areas. This has motivated the US Food and Drug Administration and the American Society of Mechanical Engineers (ASME), in partnership with medical device companies and software providers, to develop a structured approach for establishing the credibility of computational models for a specific use. Charged with this mission, the ASME V&V 40 Subcommittee on Verification and Validation (V&V) in Computational Modeling of Medical Devices developed a risk-informed credibility assessment framework; the main tenet of the framework is that the credibility requirements of a computational model should be commensurate with the risk associated with model use. This article provides an overview of the ASME V&V 40 standard and an example of the framework applied to a generic centrifugal blood pump, emphasizing how experimental evidence from in vitro testing can support computational modeling for device evaluation. Two different contexts of use for the same model are presented, which illustrate how model risk impacts the requirements on the V&V activities and outcomes.

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ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination.

Project description:Proper cell fate determination is largely orchestrated by complex gene regulatory networks centered around transcription factors. However, experimental elucidation of key transcription factors that drive cellular identity is currently often intractable. Here, we present ANANSE (ANalysis Algorithm for Networks Specified by Enhancers), a network-based method that exploits enhancer-encoded regulatory information to identify the key transcription factors in cell fate determination. As cell type-specific transcription factors predominantly bind to enhancers, we use regulatory networks based on enhancer properties to prioritize transcription factors. First, we predict genome-wide binding profiles of transcription factors in various cell types using enhancer activity and transcription factor binding motifs. Subsequently, applying these inferred binding profiles, we construct cell type-specific gene regulatory networks, and then predict key transcription factors controlling cell fate transitions using differential networks between cell types. This method outperforms existing approaches in correctly predicting major transcription factors previously identified to be sufficient for trans-differentiation. Finally, we apply ANANSE to define an atlas of key transcription factors in 18 normal human tissues. In conclusion, we present a ready-to-implement computational tool for efficient prediction of transcription factors in cell fate determination and to study transcription factor-mediated regulatory mechanisms. ANANSE is freely available at https://github.com/vanheeringen-lab/ANANSE.

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