Loimia medusa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1101159 | ENA |
REPOSITORIES: ENA
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Project description:Deciphering gene regulatory mechanisms through the analysis of high-throughput expression data is a challenging computational problem. Previous computational studies have used large expression datasets in order to resolve fine patterns of coexpression, producing clusters or modules of potentially coregulated genes. These methods typically examine promoter sequence information, such as DNA motifs or transcription factor occupancy data, in a separate step after clustering. We needed an alternative and more integrative approach to study the oxygen regulatory network in Saccharomyces cerevisiae using a small dataset of perturbation experiments. Mechanisms of oxygen sensing and regulation underlie many physiological and pathological processes, and only a handful of oxygen regulators have been identified in previous studies. We used a new machine learning algorithm called MEDUSA to uncover detailed information about the oxygen regulatory network using genome-wide expression changes in response to perturbations in the levels of oxygen, heme, Hap1, and Co2+. MEDUSA integrates mRNA expression, promoter sequence, and ChIP-chip occupancy data to learn a model that accurately predicts the differential expression of target genes in held-out data. We used a novel margin-based score to extract significant condition-specific regulators and assemble a global map of the oxygen sensing and regulatory network. This network includes both known oxygen and heme regulators, such as Hap1, Mga2, Hap4, and Upc2, as well as many new candidate regulators. MEDUSA also identified many DNA motifs that are consistent with previous experimentally identified transcription factor binding sites. Because MEDUSA's regulatory program associates regulators to target genes through their promoter sequences, we directly tested the predicted regulators for OLE1, a gene specifically induced under hypoxia, by experimental analysis of the activity of its promoter. In each case, deletion of the candidate regulator resulted in the predicted effect on promoter activity, confirming that several novel regulators identified by MEDUSA are indeed involved in oxygen regulation. MEDUSA can reveal important information from a small dataset and generate testable hypotheses for further experimental analysis.
2008-09-10 | GSE8343 | GEO
Project description:Throughout our species history, humans have created pictures. The resulting picture record reveals an overwhelming preference for depicting things with minds. This preference suggests that pictures capture something of the mind that is significant to us, albeit at reduced potency. Here, we show that abstraction dims the perceived mind, even within the same picture. In a series of experiments, people were perceived as more real, and higher in both Agency (ability to do) and Experience (ability to feel), when they were presented as pictures than when they were presented as pictures of pictures. This pattern persisted across different tasks and even when comparators were matched for identity and image size. Viewers spontaneously discriminated between different levels of abstraction during eye tracking and were less willing to share money with a more abstracted person in a dictator game. Given that mind perception underpins moral judgement, our findings suggest that depicted persons will receive greater or lesser ethical consideration, depending on the level of abstraction.
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