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 | 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. | 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. | 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 | 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 | 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 | Bougarn et al. [50] | |||
Reference dataset presenting changes in blood transcript abundance in patients with pneumonia | Â | Parnell et al. [51] | ||||
Gene Set Annotation tool. | GSAN | Third party/open | Â | Â | Allion-Benitez et al. [52] | |
Pathway Analysis tool | Ingenuity Pathway Analysis | Third party/commercial | Pathway enrichment. Used for expert curation of candidates. | Â | Â | |
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 | Â | Â | |
Drug target identification | Open targets | Third party/open | Identifies drug targets among a list of gene candidates | Â | Â | |
Retrieval of lists of immune-relevant genes | Immport | Third party/open | Provides access to curated gene lists | Â | Bhattacharya et al. [17] |