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Aortocoronary conduits may show a different inflammatory response - comparative study at transcript level

Mariusz J. Nawrocki
Mariusz J. Nawrocki
, 
Sandra Kałużna
Sandra Kałużna
, 
Karol Jopek
Karol Jopek
, 
Greg Hutchings
Greg Hutchings
, 
Bartłomiej Perek
Bartłomiej Perek
, 
Marek Jemielity
Marek Jemielity
, 
Agnieszka Malińska
Agnieszka Malińska
, 
Bartosz Kempisty
Bartosz Kempisty
, 
Paul Mozdziak
Paul Mozdziak
 y 
Michał Nowicki
Michał Nowicki
   | 29 abr 2020
Medical Journal of Cell Biology's Cover Image
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Publicado en línea: 29 abr 2020
Páginas: 24 - 34
Recibido: 21 ene 2020
Aceptado: 12 mar 2020
DOI: https://doi.org/10.2478/acb-2020-0003
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© 2020 Mariusz J. Nawrocki, Sandra Kałużna, Karol Jopek, Greg Hutchings, Bartłomiej Perek, Marek Jemielity, Agnieszka Malińska, Bartosz Kempisty, Paul Mozdziak, Michał Nowicki, published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

Heatmaps presenting differentially expressed genes involved in “cellular response to interferon-gamma”, “inflammatory response”, “interferon-gamma-mediated signaling pathway”, “response to interferon-gamma” and “positive regulation of inflammatory response” based on GO BP terms. Each row on the Y axis represents a single transcript. The red color indicates downregulated genes while the green are upregulated
Heatmaps presenting differentially expressed genes involved in “cellular response to interferon-gamma”, “inflammatory response”, “interferon-gamma-mediated signaling pathway”, “response to interferon-gamma” and “positive regulation of inflammatory response” based on GO BP terms. Each row on the Y axis represents a single transcript. The red color indicates downregulated genes while the green are upregulated

Figure 2

The bar plot presenting z-scores of processes involved in inflammatory response
The bar plot presenting z-scores of processes involved in inflammatory response

Figure 3

The circular scatter plots of differentially expressed genes involved in “cellular response to interferon-gamma”, “inflammatory response”, “interferon-gamma-mediated signaling pathway”, “response to interferon-gamma” and “positive regulation of inflammatory response” GO BP terms. Each dot represents a single gene. The z-scores were presented as segments of inner circles
The circular scatter plots of differentially expressed genes involved in “cellular response to interferon-gamma”, “inflammatory response”, “interferon-gamma-mediated signaling pathway”, “response to interferon-gamma” and “positive regulation of inflammatory response” GO BP terms. Each dot represents a single gene. The z-scores were presented as segments of inner circles

Figure 4

The dendrogram of differentially expressed genes involved in “cellular response to interferon-gamma”, “inflammatory response”, “interferon-gamma-mediated signaling pathway”, “response to interferon-gamma” and “positive regulation of inflammatory response” GO BP terms. The DEGs were clustered based on their logFC values
The dendrogram of differentially expressed genes involved in “cellular response to interferon-gamma”, “inflammatory response”, “interferon-gamma-mediated signaling pathway”, “response to interferon-gamma” and “positive regulation of inflammatory response” GO BP terms. The DEGs were clustered based on their logFC values

Figure 5

Analysis of enriched gene ontological groups involved in inflammatory response. The network plot presenting the linkages of genes and GO BP terms
Analysis of enriched gene ontological groups involved in inflammatory response. The network plot presenting the linkages of genes and GO BP terms

Figure 6

Heatmap presenting the relationship between genes and selected GO BP terms. The yellow color of tiles indicates the absence of logFC values
Heatmap presenting the relationship between genes and selected GO BP terms. The yellow color of tiles indicates the absence of logFC values

Figure 7

Interaction network of proteins encoded by DEGs belonging to “cellular response to interferon-gamma”, “inflammatory response”, “interferon-gamma-mediated signaling pathway”, “response to interferon-gamma” and “positive regulation of inflammatory response” GO BP terms. The network was generated by STRING software. Network nodes represent proteins. Empty nodes indicate proteins of unknown 3D structure
Interaction network of proteins encoded by DEGs belonging to “cellular response to interferon-gamma”, “inflammatory response”, “interferon-gamma-mediated signaling pathway”, “response to interferon-gamma” and “positive regulation of inflammatory response” GO BP terms. The network was generated by STRING software. Network nodes represent proteins. Empty nodes indicate proteins of unknown 3D structure

Figure 8

Reactome FI network for “Immune response”. “--->” indicates activating/catalyzing, “-“ FIs extracted from complexes or inputs and “---” predicted FIs
Reactome FI network for “Immune response”. “--->” indicates activating/catalyzing, “-“ FIs extracted from complexes or inputs and “---” predicted FIs

Figure 9

Reactome FI network for “Interferon-gamma-mediated signaling pathway”. “--->” indicates activating/catalyzing, “-|” for inhibition, “-“ FIs extracted from complexes or inputs and “---” predicted FIs
Reactome FI network for “Interferon-gamma-mediated signaling pathway”. “--->” indicates activating/catalyzing, “-|” for inhibition, “-“ FIs extracted from complexes or inputs and “---” predicted FIs

The 10 most significantly upregulated and 10 most significantly downregulated genes involved in inflammatory response

Gene symbolGene nameFold changeAdj. p.val
TNFRSF11Btumor necrosis factor receptor superfamily, member 11b4.74<0.01
CCL4L1chemokine (C-C motif) ligand 4—like 14.53<0.01
SELEselectin E3.760.01
PTGER3prostaglandin E receptor 3 (subtype EP3)3.53<0.01
CCL8chemokine (C-C motif) ligand 83.23<0.01
JAK2Janus kinase 23.18<0.01
TAC1tachykinin, precursor 13.17<0.01
S100A9S100 calcium binding protein A93.150.02
SPP1secreted phosphoprotein 12.97<0.01
TGM2transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)2.58<0.01
CCL14chemokine (C-C motif) ligand 14-2.43<0.01
BMP6bone morphogenetic protein 6-2.45<0.01
CFHcomplement factor H-2.63<0.01
CD44CD44 molecule (Indian blood group)-2.73<0.01
C7complement component 7-2.78<0.01
TRILTLR4 interactor with leucine-rich repeats-2.95<0.01
PDE2Aphosphodiesterase 2A, cGMP-stimulated-2.98<0.01
NLRC5NLR family, CARD domain containing 5-3.16<0.01
CNR1cannabinoid receptor 1 (brain)-3.27<0.01
P2RX1purinergic receptor P2X, ligand-gated ion channel, 1-6.48<0.01
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