Dataset Information

Network inference of pal-1 lineage-specific regulation in the C. elegans embryo by structural equation modeling.

ABSTRACT: The elucidation of spatial and temporal control during developmental stages is one of the central tasks for systems biology, and a variety of intracellular factors are known as regulators for specific gene expression. The activity information of those various factors is not directly reflected in their gene expression profiles. Hence, a method based on Structural Equation Modeling (SEM) is described. SEM can include the latent variables within the constructed model and infer the relationships among latent and observed variables, as a network model. An improved SEM approach for the construction of an optimal model is applied to infer the regulatory network for the determination of C lineage fate in C. elegans development. The inferred network model shows that the 13 analysed transcription factor genes were regulated by several other factors in addition to pal-1 expression. The other regulatory factors are those involved in protein accumulation and localization as important regulatory factors for normal development. Those regulatory factors were regulated sequentially in the network model. The regulation of the known pal-1 regulated genes was dependent on this sequential control of the regulatory factors. The interpretation of the network model shows insights to the complex regulation occurring during the C lineage determination by pal-1.

SUBMITTER: Aburatani S

PROVIDER: S-EPMC3449367 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Network inference of pal-1 lineage-specific regulation in the C. elegans embryo by structural equation modeling.

Aburatani Sachiyo S

Bioinformation 20120721 14

The elucidation of spatial and temporal control during developmental stages is one of the central tasks for systems biology, and a variety of intracellular factors are known as regulators for specific gene expression. The activity information of those various factors is not directly reflected in their gene expression profiles. Hence, a method based on Structural Equation Modeling (SEM) is described. SEM can include the latent variables within the constructed model and infer the relationships amo ...[more]

PMID: 23055605

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Project description:Firearm homicides disproportionately affect Black communities. Redlining - discriminatory lending practices of the early 20th century - are associated with current increased rates of firearm violence. Poverty and concentrated disadvantage are also associated with firearm violence. The interaction of these factors with racist redlining housing practices remains unclear. We used generalized structural equation modeling to characterize the mediators through which redlining practices of the 1930s led to present rates of firearm violence in Boston using a negative binomial model. Principle component analysis was used to create four distinct mediating variables representing census block socioeconomic and built environment information, while reducing dimensionality. We calculated the direct effect between harmful (Red and Yellow) vs beneficial (Green) designations and firearm incident rate, indirect effect between redlining designation and firearm incident rate through each mediating variable, and the total effect. The percentage mediation of each mediator was subsequently calculated. Red and Yellow areas of Boston were associated with an 11•1 (95% CI 5•5,22•4) and 11•4 (5•7,22•8) increased incident rate of shooting when compared to Green. In the pathway between Red designation and firearm incident rate, poverty and poor educational attainment mediated 20% of the interaction, share of rented housing mediated 8%, and Black share of the population 3%. In the pathway between Yellow designation and firearm incident rate, poverty and poor educational attainment mediated 16% of the association, and Black share of the population mediated 13%. Redlining practices of the 1930s potentially contribute to increased rates of firearm violence through changes to neighborhood environments, namely through preclusion from homeownership, poverty, poor educational attainment, and concentration (i.e. segregation) of Black communities. These downstream mediating factors serve as points for policy interventions to address urban firearm violence. Michael Poulson and Miriam Neufeld were supported by T32 Training Grants (HP10028, GM86308).

Dataset Information

Network inference of pal-1 lineage-specific regulation in the C. elegans embryo by structural equation modeling.

Publications

Network inference of pal-1 lineage-specific regulation in the C. elegans embryo by structural equation modeling.

Similar Datasets

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