Skip to main content

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: https://prezi.com/view/zYCSLyo0nvJTwjfJkJqb/
A28: https://prezi.com/view/7lbgGwfiNflffqQzvL14/)
Part 1: https://youtu.be/_7sNE3e5W5g
Part 2: https://youtu.be/I6wHrrmbet4
Part 3: https://youtu.be/iHnM7OH_nw8
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. https://drinchai.shinyapps.io/COVID_19_project/ https://youtu.be/XhQZj9mm2ME Present work
Gen3 app In house/open Provides access to 16 reference patient cohorts datasets https://drinchai.shinyapps.io/dc_gen3_module_analysis/# https://youtu.be/y__7xKJo5e4 Altman et al. [7]
RSV app In house/open Provides access to six public RSV blood transcriptome datasets. https://drinchai.shinyapps.io/RSV_Meta_Module_analysis/ https://youtu.be/htNSMreM8es 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 http://sepsis.gxbsidra.org/dm3/geneBrowser/list https://youtu.be/D1rGYfVSAoM Toufiq et al. (in preparation), and Speake et al. [48]
A reference dataset presenting transcript abundance profiles across purified leukocyte populations http://sepsis.gxbsidra.org/dm3/geneBrowser/show/4000098 Linsley et al. [49]
Reference dataset presenting the response to in vitro blood stimulations http://sepsis.gxbsidra.org/dm3/geneBrowser/show/4000152 Obermoser et al. [22]
GXB Acute Respiratory Infection In house/open 34 curated datasets relevant to acute respiratory infections http://vri1.gxbsidra.org/dm3/geneBrowser/list Bougarn et al. [50]
Reference dataset presenting changes in blood transcript abundance in patients with pneumonia http://vri1.gxbsidra.org/dm3/miniURL/view/Mh   Parnell et al. [51]
Gene Set Annotation tool. GSAN Third party/open   https://gsan.labri.fr/   Allion-Benitez et al. [52]
Pathway Analysis tool Ingenuity Pathway Analysis Third party/commercial Pathway enrichment. Used for expert curation of candidates. https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/   
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 https://www.acumenta.com/generetriever   
Drug target identification Open targets Third party/open Identifies drug targets among a list of gene candidates https://www.targetvalidation.org/   
Retrieval of lists of immune-relevant genes Immport Third party/open Provides access to curated gene lists https://immport.org/shared/home   Bhattacharya et al. [17]
\