The dkNET Hypothesis Center Signaling Pathways Project (SPP) is a free, open source tool for bench scientists to generate research hypotheses using SPP consensomes and was used for the recent bioRxiv publication, A transcriptional regulatory atlas of coronavirus infection of human cells. In this webinar, the SPP project lead, Dr Neil McKenna, described a number of important facets of this study, including:
1. Identifying human genes most consistently transcriptionally responsive to coronavirus infection
2. Inferring human signaling pathway nodes implicated in the cellular response to coronavirus infection
3. Strategies for generating hypotheses for connections between your research area of interest and coronavirus infection.
Presenter: Neil McKenna, PhD, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
dkNET Webinar: dkNET Hypothesis Center - Signaling Pathways Project Live Demo
1. The Signaling Pathways Project:
The Signaling Pathways Project, An Integrated ‘Omics Knowledgebase
For Mammalian Cellular Signaling Pathways
Scott Ochsner, PhD & Neil McKenna, PhD
Department of Molecular and Cellular Biology
Baylor College of Medicine, Houston TX
2. The Signaling Pathways Project: making cell signaling ‘omics
datasets FAIR for bench researchers
FAIR: Findable, Accessible, Interoperable, Re-usable
3. Signaling pathways involve physical and functional interactions
between distinct classes of signaling pathway nodes
4. Transcriptomic
Expression array & RNA-Seq
Cistromic
ChIP-Seq
Receptors
Enzymes
Transcription
Factors
Co-nodes
Signaling Pathways Project (SPP): two universes of biocurated
transcriptional data points mapped to cell signaling pathway nodes
SPP node types
Hs
Mm
Rn
Hs
Mm Mm
5. Consensomes: lists of genes ranked by their transcriptional
responsiveness to cellular signaling pathway nodes
Transcriptomic Cistromic (ChIP-Seq)
Human insulin receptor family
6. Consensomes: lists of genes ranked by their transcriptional
responsiveness to cellular signaling pathway nodes
7. Consensomes: lists of genes ranked by their transcriptional
responsiveness to cellular signaling pathway nodes
9. Signaling Pathways Project (SPP) and the coronavirus crisis
• How can we leverage SPP to help researchers formulate hypotheses
around the impact of CoV infection on human cellular signaling pathways?
• Biocuration of existing archived CoV infection transcriptomic datasets
• 8 Severe Acute Respiratory Syndrome coronavirus (SARS-CoV-1)
• 13 Middle East Respiratory Syndrome CoV (MERS-CoV)
• 1 SARS-CoV-2 (initially, now 5 and counting…)
• 3 human coronavirus HCoV 229E
• 6 Influenza A Virus
• Using these datasets we generated five transcriptomic consensomes (Pan-
CoV, SARS-CoV-2, SARS-CoV-2, MERS and IAV)
11. SPP consensomes identify high confidence transcriptional
footprints for cellular signaling pathway nodes & CoV infection
12. Pan CoV infection Consensome
SPP consensomes identify high confidence transcriptional
footprints for cellular signaling pathway nodes & CoV infection
13. Node consensome CoV infection consensome
Significant overlap between node and a CoV consensome is
evidence of a role for that node in the cellular response to infection
14. Node consensome CoV infection consensome
Overlap not significantly different from random (OR = 1, p > 0.05)
Significant overlap between node and a CoV consensome is
evidence of a role for that node in the cellular response to infection
15. Node consensome CoV infection consensome
Overlap significantly different from random (OR = > 1, p < 0.05)
Significant overlap between node and a CoV consensome is
evidence of a role for that node in the cellular response to infection
16. Pathway nodes with known roles in CoV and/or viral infection
have expanded transcriptional footprints in the Pan-CoV consensome
17. Pathway nodes with known roles in CoV and/or viral infection
have expanded transcriptional footprints in the Pan-CoV consensome
18. Pathway nodes with known roles in CoV and/or viral infection
have expanded transcriptional footprints in the Pan-CoV consensome
19. Pathway nodes with known roles in CoV and/or viral infection
have expanded transcriptional footprints in the Pan-CoV consensome
20. Pathway nodes with known roles in CoV and/or viral infection
have expanded transcriptional footprints in the Pan-CoV consensome
21. Pathway nodes with known roles in CoV and/or viral infection
have expanded transcriptional footprints in the Pan-CoV consensome
22. Pathway nodes with known roles in CoV and/or viral infection
have expanded transcriptional footprints in the Pan-CoV consensome
23. Pathway nodes with known roles in CoV and/or viral infection
have expanded transcriptional footprints in the Pan-CoV consensome
24. Pathway nodes with known roles in CoV and/or viral infection
have expanded transcriptional footprints in the Pan-CoV consensome
25. Pathway nodes with known roles in CoV and/or viral infection
have expanded transcriptional footprints in the Pan-CoV consensome
26. Pathway nodes with known roles in CoV and/or viral infection
have expanded transcriptional footprints in the Pan-CoV consensome
29. Sutton et al. (2020) NEJM 10.1056/NEJMc2009316
Is there a link between PR antagonism of interferon signaling and
asymptomatic presentation in SARS-CoV-2 in pregnancy?
30. Pathway nodes mediating epithelial to mesenchymal transition
have SARS-CoV-2-specific transcriptional footprint expansions
31. Pathway nodes mediating epithelial to mesenchymal transition
have SARS-CoV-2-specific transcriptional footprint expansions
32. Pathway nodes mediating epithelial to mesenchymal transition
have SARS-CoV-2-specific transcriptional footprint expansions
33. Pathway nodes mediating epithelial to mesenchymal transition
have SARS-CoV-2-specific transcriptional footprint expansions
34. Epithelial to mesenchymal transition contributes to pathological
conditions in SARS-CoV-2 infection target organ systems
40. Thank you
National Institute of Diabetes, Digestive & Kidney Diseases (NIDDK)
NIDDK Information Network (dkNET)
American Thyroid Association
www.signalingpathways.org
@sigpathproject