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In search of markers useful for evaluation of graft patency - molecular analysis of ‘muscle system process’ for internal thoracic artery and saphenous vein conduits

Sandra Kałużna
Sandra Kałużna
, 
Mariusz J. Nawrocki
Mariusz J. Nawrocki
, 
Karol Jopek
Karol Jopek
, 
Greg Hutchings
Greg Hutchings
, 
Bartłomiej Perek
Bartłomiej Perek
, 
Marek Jemielity
Marek Jemielity
, 
Bartosz Kempisty
Bartosz Kempisty
, 
Agnieszka Malińska
Agnieszka Malińska
, 
Paul Mozdziak
Paul Mozdziak
 et 
Michał Nowicki
Michał Nowicki
   | 29 avr. 2020
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Publié en ligne: 29 avr. 2020
Pages: 12 - 23
Reçu: 11 janv. 2020
Accepté: 02 mars 2020
DOI: https://doi.org/10.2478/acb-2020-0002
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© 2020 Sandra Kałużna, Mariusz J. Nawrocki, Karol Jopek, Greg Hutchings, Bartłomiej Perek, Marek Jemielity, Bartosz Kempisty, Agnieszka Malińska, 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 “muscle cell proliferation”, “muscle contraction”, “muscle system process”, “regulation of smooth muscle cell proliferation” and “smooth muscle cell proliferation” 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 “muscle cell proliferation”, “muscle contraction”, “muscle system process”, “regulation of smooth muscle cell proliferation” and “smooth muscle cell proliferation” 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 circular scatter plots of differentially expressed genes involved in “muscle cell proliferation”, “muscle contraction”, “muscle system process”, “regulation of smooth muscle cell proliferation” and “smooth muscle cell proliferation” 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 “muscle cell proliferation”, “muscle contraction”, “muscle system process”, “regulation of smooth muscle cell proliferation” and “smooth muscle cell proliferation” GO BP terms. Each dot represents a single gene. The z-scores were presented as segments of inner circles

Figure 3

The dendrogram of differentially expressed genes involved in “muscle cell proliferation”, “muscle contraction”, “muscle system process”, “regulation of smooth muscle cell proliferation” and “smooth muscle cell proliferation” GO BP terms. The DEGs were clustered based on their logFC values
The dendrogram of differentially expressed genes involved in “muscle cell proliferation”, “muscle contraction”, “muscle system process”, “regulation of smooth muscle cell proliferation” and “smooth muscle cell proliferation” GO BP terms. The DEGs were clustered based on their logFC values

Figure 4

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

Figure 5

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 6

Interaction network of proteins encoded by DEGs belonging to “muscle cell proliferation”, “muscle contraction”, “muscle system process”, “regulation of smooth muscle cell proliferation” and “smooth muscle cell proliferation” GO BP terms. The network was generated by STRING software. Network nodes represent proteins, while empty nodes indicate proteins of unknown 3D structure
Interaction network of proteins encoded by DEGs belonging to “muscle cell proliferation”, “muscle contraction”, “muscle system process”, “regulation of smooth muscle cell proliferation” and “smooth muscle cell proliferation” GO BP terms. The network was generated by STRING software. Network nodes represent proteins, while empty nodes indicate proteins of unknown 3D structure

Figure 7

Reactome FI networks between differentially expressed genes belonging to the “muscle cell proliferation”, “muscle contraction”, “muscle system process”, “regulation of smooth muscle cell proliferation” and “smooth muscle cell proliferation” GO BP terms. “--->” indicates activating/catalyzing, “-|” for inhibition, “-“ FIs extracted from complexes or inputs and “---” predicted FIs
Reactome FI networks between differentially expressed genes belonging to the “muscle cell proliferation”, “muscle contraction”, “muscle system process”, “regulation of smooth muscle cell proliferation” and “smooth muscle cell proliferation” GO BP terms. “--->” indicates activating/catalyzing, “-|” for inhibition, “-“ FIs extracted from complexes or inputs and “---” predicted FIs

Figure 8

Pathway graph of “calcium signaling pathway” based on KEGG database. The red color indicates parts of the pathway that are upregulated in internal thoracic artery conduit while the green color represents components upregulated in saphenous vein conduit
Pathway graph of “calcium signaling pathway” based on KEGG database. The red color indicates parts of the pathway that are upregulated in internal thoracic artery conduit while the green color represents components upregulated in saphenous vein conduit

The 10 most significantly upregulated and 10 most significantly downregulated genes involved in muscle system process

Gene symbolGene nameFold changeAdj. p.val
ACTN2actinin, alpha 210.99<0.05
RBPMS2RNA binding protein with multiple splicing 26.57<0.05
NR4A3nuclear receptor subfamily 4, group A, member 35.72<0.05
KCNA5potassium voltage-gated channel, shaker-related subfamily, member 55.46<0.05
NPR3natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)5.30<0.05
PTGER3prostaglandin E receptor 3 (subtype EP3)3.53<0.05
RBP4retinol binding protein 4, plasma3.23<0.05
OGNosteoglycin3.23<0.05
JAK2Janus kinase 23.18<0.05
MYH11myosin, heavy chain 11, smooth muscle3.17<0.05
PPARGC1Aperoxisome proliferator-activated receptor gamma, coactivator 1 alpha-2.20<0.05
NDRG4NDRG family member 4-2.22<0.05
HTR2A5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled-2.32<0.05
ITGA2integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)-2.38<0.05
HTR2B5-hydroxytryptamine (serotonin) receptor 2B, G protein-coupled-2.64<0.05
SCN4Bsodium channel, voltage-gated, type IV, beta subunit-3.13<0.05
MYOTmyotilin-3.39<0.05
DESdesmin-4.44<0.05
KCNH2potassium voltage-gated channel, subfamily H (eag-related), member 2-6.25<0.05
P2RX1purinergic receptor P2X, ligand-gated ion channel, 1-6.48<0.05
eISSN:
2544-3577
Langue:
Anglais
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Sujets de la revue:
Life Sciences, Molecular Biology, Biochemistry
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