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Differential expression pattern of genes involved in oxygen metabolism in epithelial oviductal cells during primary in vitro culture

Medical Journal of Cell Biology
Volume 7 (2019): Issue 2 (September 2019)
By:
Open Access
|Oct 2019

Figures & Tables

Figure 1

Heat map representation of differentially expressed genes belonging to the to “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” 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 to “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” 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 “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” GO BP terms. The outer circle shows a scatter plot for each term of the fold change of the assigned genes. Green circles display up- regulation and red ones down- regulation. 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 “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” GO BP terms. The outer circle shows a scatter plot for each term of the fold change of the assigned genes. Green circles display up- regulation and red ones down- regulation. 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 “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” 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 “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” 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 “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” 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 “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” 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 belongs to the “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” 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 belongs to the “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” GO BP terms. The intensity of the edges reflects the strength of interaction score

Figure 6

Functional interaction (FI) between 20 chosen differently expressed genes that belongs to the “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” GO BP terms. In following figure “->” stands for activating/catalyzing, “-|” for inhibition, “-” for FIs extracted from complexes or inputs, and “---” for predicted FIs
Functional interaction (FI) between 20 chosen differently expressed genes that belongs to the “cellular response to oxidative stress”, “cellular response to oxygen-containing compound”, “cellular response to oxygen levels” and “cellular response to reactive oxygen species” GO BP terms. In following figure “->” stands for activating/catalyzing, “-|” for inhibition, “-” for FIs extracted from complexes or inputs, and “---” for predicted FIs

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

GENE SYMBOLRATIO D7/D1RATIO D15/D1RATIO D30/D1ADJUSTED P.VALUE D7/D1ADJUSTED P.VALUE D15/D1ADJUSTED P.VALUE D30/D1MEAN RATIO
AQP9-4,009-7,510-69,2472,57E-042,80E-055,88E-07-26,922
MUC1-4,154-28,786-47,1474,67E-059,76E-072,44E-07-26,695
EDNRB-2,719-11,232-53,9717,06E-046,74E-064,60E-07-22,641
IL24-11,995-16,079-14,0069,50E-063,21E-061,76E-06-14,027
CYP24A1-6,704-3,398-25,2632,69E-051,36E-047,91E-07-11,788
KLF4-4,866-11,123-17,4044,71E-053,93E-061,01E-06-11,131
PIM1-2,278-7,702-14,7548,42E-047,24E-061,14E-06-8,245
SNAI2-5,442-7,434-7,6884,11E-041,29E-047,85E-05-6,854
LPAR1-2,576-3,932-5,9534,96E-036,50E-041,17E-04-4,154
IRS1-3,201-4,110-4,2546,44E-051,52E-058,37E-06-3,855
ABCA16,3135,55710,3363,95E-053,12E-054,36E-067,402
TNC6,5738,3528,7731,83E-054,91E-062,42E-067,899
GAS64,3369,49516,7551,66E-051,63E-062,93E-0710,195
EPAS17,6306,65516,8288,57E-065,17E-065,84E-0710,371
MMP25,01411,11519,1071,73E-051,68E-063,42E-0711,745
COL5A25,87820,35924,5397,45E-067,45E-072,31E-0716,925
NOX411,05621,12832,0714,90E-069,73E-072,31E-0721,418
FBN13,69227,54762,8491,51E-041,63E-063,07E-0731,363
PRLR8,16922,94573,1347,45E-069,73E-072,31E-0734,749
COL1A215,57356,37661,3293,63E-067,45E-072,31E-0744,426
DOI: https://doi.org/10.2478/acb-2019-0009 | Journal eISSN: 2544-3577
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Language: English
Page range: 66 - 76
Submitted on: Aug 15, 2019
Accepted on: Sep 11, 2019
Published on: Oct 12, 2019
Published by: Foundation for Cell Biology and Molecular Biology
In partnership with: Paradigm Publishing Services
Publication frequency: 4 times per year
Keywords:
oviductal epithelial cells,
culture,
oxygen metabolism,
transcriptom
Related subjects:
Life sciences,
Molecular biology,
Biochemistry

© 2019 Katarzyna Stefańska, Sandra Knap, Magdalena Kulus, Ievgenia Kocherova, Piotr Celichowski, Michal Jeseta, Marie Machatkova, Dorota Bukowska, Paweł Antosik, published by Foundation for Cell Biology and Molecular Biology
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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