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Table 3 Resources used for annotation and interpretation

From: A modular framework for the development of targeted Covid-19 blood transcript profiling panels

Platform/Use Name Source Notes Link Demo video Ref.
Interactive presentations (Prezi) Exploration of aggregated annotations/curation/capture interpretation of functional relevance in the context of Covid-19 disease Covid-19 Module Sets annotation framework In house/open See Fig. 5 for details A31:
Part 1:
Part 2:
Part 3:
Present work
R Shiny Web Applications/Exploration of module-level and gene-level blood transcriptome profiling data.
Design and export of custom plots to populate the annotation framework.
Covid-19 app In house/open Provides access to two Covid-19 blood transcript profiling datasets. More will be added as they become available. Present work
Gen3 app In house/open Provides access to 16 reference patient cohorts datasets Altman et al. [7]
RSV app In house/open Provides access to six public RSV blood transcriptome datasets. Rinchai et al. [18]
Gene Expression Browser (GXB) Interactive browsing of expression profiles for individual transcripts. Themed curated dataset collections have been created. GXB sepsis collection In house/open Makes 93 curated datasets relevant to sepsis Toufiq et al. (in preparation), and Speake et al. [48]
A reference dataset presenting transcript abundance profiles across purified leukocyte populations Linsley et al. [49]
Reference dataset presenting the response to in vitro blood stimulations Obermoser et al. [22]
GXB Acute Respiratory Infection In house/open 34 curated datasets relevant to acute respiratory infections Bougarn et al. [50]
Reference dataset presenting changes in blood transcript abundance in patients with pneumonia   Parnell et al. [51]
Gene Set Annotation tool. GSAN Third party/open   Allion-Benitez et al. [52]
Pathway Analysis tool Ingenuity Pathway Analysis Third party/commercial Pathway enrichment. Used for expert curation of candidates.   
Accumenta Biotech LiteratureLab
Literature profiling and keyword enrichment tool
LitLab Gene Retreiver Collaboration with Third party/commercial Retrieves genes from a collection of literature records provided by the user   
Drug target identification Open targets Third party/open Identifies drug targets among a list of gene candidates   
Retrieval of lists of immune-relevant genes Immport Third party/open Provides access to curated gene lists   Bhattacharya et al. [17]