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FAIR Functional Enrichment: Assessing and Modelling Provenance in Omics Results

This investigation serves as supplementary material for a SWAT4HCLS publication that describes minimum metadata and provenance requirements for reproducible enrichment analysis results.

Functional enrichment analysis is an essential downstream process in high throughput omics studies, such as transcriptomics and proteomics. By using the Gene Ontology (GO) and its annotations (GOA), underlying functional patterns of over-representation can be identified, leading to ...

Submitter: Yi Chen

Studies: FAIR Functional Enrichment

Assays: FAIR Functional Enrichment

Snapshots: No snapshots

Created: 28th Nov 2022 at 13:01, Last updated: 13th Jan 2023 at 08:21

Footprint based analysis and causal network contextualisation in SARS-CoV-2 infected A549 cell line

COVID-19 Disease Map

We further used the transcriptome dataset from the GEO database with accession number GSE147507 (Blanco-Melo et al., 2020) to extract the series number 5 from the dataset, consisting of 2 conditions in triplicate, A549 cells treated with a mock and A549 infected with SARS-CoV-2, measured 24 hours after treatment. Phosphoproteomic data of mock-treated and SARS-CoV2 infected cells were extracted from (Stukalov et al., 2020). We then applied our pipeline described in M&M X. This work notably ...

Submitter: Aurélien Dugourd

Studies: Footprint based analysis and causal network contextualisation in SARS-Co...

Assays: No Assays

Snapshots: No snapshots

Created: 19th Apr 2021 at 11:13

From steady-state to synchronized yeast glycolytic oscillations

Yeast glycolytic oscillations