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Nucleotide, ribonucleotide and ribonucleoside binding belongs to differentially expressed genes in porcine epithelial oviductal cells during longterm primary cultivation

Mariusz J. Nawrocki
Mariusz J. Nawrocki
, 
Rafał Sibiak
Rafał Sibiak
, 
Sandra Kałużna
Sandra Kałużna
, 
Maciej Brązert
Maciej Brązert
, 
Piotr Celichowski
Piotr Celichowski
, 
Leszek Pawelczyk
Leszek Pawelczyk
, 
Lisa Moncrieff
Lisa Moncrieff
, 
Bartosz Kempisty
Bartosz Kempisty
 et 
Paul Mozdziak
Paul Mozdziak
   | 21 déc. 2019
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Publié en ligne: 21 déc. 2019
Pages: 161 - 169
Reçu: 03 nov. 2019
Accepté: 08 déc. 2019
DOI: https://doi.org/10.2478/acb-2019-0022
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© 2019 Mariusz J. Nawrocki, Rafał Sibiak, Sandra Kałużna, Maciej Brązert, Piotr Celichowski, Leszek Pawelczyk, Lisa Moncrieff, Bartosz Kempisty, Paul Mozdziak, published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

Heat map representation of differentially expressed genes belonging to the “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. Arbitrary signal intensity acquired from microarray analysis is represented by colours (green, higher; red, lower expression). Log2 signal intensity values for any single gene were resized to Row Z-Score scale (from -2, the lowest expression to +2, the highest expression for single gene). The 20 genes selected to this publication was marked green for upregulation and red for downregulation
Heat map representation of differentially expressed genes belonging to the “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. Arbitrary signal intensity acquired from microarray analysis is represented by colours (green, higher; red, lower expression). Log2 signal intensity values for any single gene were resized to Row Z-Score scale (from -2, the lowest expression to +2, the highest expression for single gene). The 20 genes selected to this publication was marked green for upregulation and red for downregulation

Figure 2

The circle plot showing the differently expressed genes and z-score of the “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The outer circle shows a scatter plot for each term of the fold change of the assigned genes. Green circles display upregulation and red ones downregulation. The inner circle shows the z-score of each GO BP term. The width of the each bar corresponds to the number of genes within GO BP term and the color corresponds to the z-score
The circle plot showing the differently expressed genes and z-score of the “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The outer circle shows a scatter plot for each term of the fold change of the assigned genes. Green circles display upregulation and red ones downregulation. The inner circle shows the z-score of each GO BP term. The width of the each bar corresponds to the number of genes within GO BP term and the color corresponds to the z-score

Figure 3

The representation of the mutual relationship of differently expressed genes that belongs to 20 chosen genes from “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The ribbons indicate which gene belongs to which categories. The middle circle represents logarithm from fold change (LogFC) between D7/D1, D15/D1 and D30/D1 respectively. The color of each block corresponds to the LogFC of each gene (green – upregulated, red – downregulated). The genes were sorted by logFC from most to least changed gene
The representation of the mutual relationship of differently expressed genes that belongs to 20 chosen genes from “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The ribbons indicate which gene belongs to which categories. The middle circle represents logarithm from fold change (LogFC) between D7/D1, D15/D1 and D30/D1 respectively. The color of each block corresponds to the LogFC of each gene (green – upregulated, red – downregulated). The genes were sorted by logFC from most to least changed gene

Figure 4

Heatmap showing the gene occurrence between chosen 20 differently expressed genes that belongs to “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The yellow color is associated with gene occurrence in the GO Term. The intensity of the color is corresponding to amount of GO BP terms that each gene belongs to
Heatmap showing the gene occurrence between chosen 20 differently expressed genes that belongs to “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The yellow color is associated with gene occurrence in the GO Term. The intensity of the color is corresponding to amount of GO BP terms that each gene belongs to

Figure 5

STRING-generated interaction occurrence between 20 chosen differently expressed genes that belong to the “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The intensity of the edges reflects the strength of interaction score
STRING-generated interaction occurrence between 20 chosen differently expressed genes that belong to the “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The intensity of the edges reflects the strength of interaction score

Gene symbols, fold change in expression ratio, Entrez gene IDs, corrected p values and mean value of fold change ratio of the 20 chosen differentially expressed, studied genes

GENE SYMBOLRATIO D7/D1RATIO D30/D1RATIO D15/D1ADJUSTED P.VALUE D7/D1ADJUSTED P.VALUE D15/D1ADJUSTED P.VALUE D30/D1ENTREZ GENE IDMEAN RATIO
OASL-19.013577-19.59127971-20.336183352.69E-051.34E-057.93E-06595119-19.64701335
PIM1-2.278169547-7.702016846-14.754105230.0008419077.24E-061.14E-06100157844-8.244763875
RAB27A-2.438418171-6.421074057-12.173069460.0002406884.70E-067.36E-07606749-7.010853897
ERBB3-3.700854877-8.072357208-8.4746852384.67E-053.53E-061.48E-06----6.749299107
DDX60-9.539122077-5.148779-4.6900320077.61E-050.0002441710.000232065----6.459311028
NAV3-2.570715662-3.817701681-12.083441850.0050323430.0007252752.01E-05----6.157286398
MX2-8.476906188-5.025767174-2.8641640983.11E-056.87E-050.000433456396893-5.455612486
MCM4-1.824811573-2.553654794-11.202764010.0016727660.0001406478.81E-07100156398-5.193743459
DHX58-6.093081701-5.06259312-3.5196354782.24E-051.83E-054.23E-05100524520-4.891770099
OAS1-4.734227264-4.803325858-4.5796449310.0006377140.0004545790.00038381----4.705732684
CFTR5.9300964175.9712435533.5807261414.73E-052.79E-050.0001032064031545.160688703
BVES5.0848352356.8894512874.9584691650.0001647894.63E-057.99E-051001531065.644251896
NUAK15.900044387.6877989424.2054187882.17E-055.48E-061.88E-051005236695.93108737
PANK17.8555618993.4916737057.1586499317.45E-063.27E-052.08E-061001546506.168628512
ACAA24.8213472966.2239741047.7910046251.04E-053.05E-068.03E-071003129596.278775342
FGFR14.5997141055.6507750558.9429760691.33E-053.63E-066.88E-071001532486.397821743
P2RX76.1651423438.5220423545.7953978352.69E-056.72E-061.03E-054976236.827527511
KIF236.4968599847.1059650667.1047519130.0006469770.0003819780.0002712141005221166.902525654
ABCA16.3133960765.55674690110.335579183.95E-053.12E-054.36E-061001521127.401907384
ACTA25.22524140512.5408405430.246218283.15E-053.09E-064.37E-0773361516.00410008
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Life Sciences, Molecular Biology, Biochemistry
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