Open Access

Genes regulating biochemical pathways of oxygen metabolism in porcine oviductal epithelial cells during long-term IVC

Ievgeniia Kocherova
Ievgeniia Kocherova
, 
Maciej Brązert
Maciej Brązert
, 
Patrycja Sujka-Kordowska
Patrycja Sujka-Kordowska
, 
Aneta Konwerska
Aneta Konwerska
, 
Magdalena Kulus
Magdalena Kulus
, 
Błażej Chermuła
Błażej Chermuła
, 
Piotr Celichowski
Piotr Celichowski
, 
Hanna Piotrowska-Kempisty
Hanna Piotrowska-Kempisty
, 
Paweł Antosik
Paweł Antosik
, 
Dorota Bukowska
Dorota Bukowska
, 
Małgorzata Bruska
Małgorzata Bruska
, 
Leszek Pawelczyk
Leszek Pawelczyk
, 
Maciej Zabel
Maciej Zabel
, 
Michał Nowicki
Michał Nowicki
, 
Bartosz Kempisty
Bartosz Kempisty
 and 
Michal Jeseta
Michal Jeseta
   | Oct 12, 2019
Medical Journal of Cell Biology's Cover Image
About this article
Previous Article
Next Article
Cite
Published Online: Oct 12, 2019
Page range: 39 - 47
Received: Jul 21, 2019
Accepted: Aug 18, 2019
DOI: https://doi.org/10.2478/acb-2019-0006
Keywords
© 2019 Ievgeniia Kocherova, Maciej Brązert, Patrycja Sujka-Kordowska, Aneta Konwerska, Magdalena Kulus, Błażej Chermuła, Piotr Celichowski, Hanna Piotrowska-Kempisty, Paweł Antosik, Dorota Bukowska, Małgorzata Bruska, Leszek Pawelczyk, Maciej Zabel, Michał Nowicki, Bartosz Kempisty, Michal Jeseta, 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 “cellular response to oxidative stress” and “cellular response to oxygen-containing compound” 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 “cellular response to oxidative stress” and “cellular response to oxygen-containing compound” 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” and “cellular response to oxygen-containing compound” 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” and “cellular response to oxygen-containing compound” 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” and “cellular response to oxygen-containing compound” 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” and “cellular response to oxygen-containing compound” 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” and “cellular response to oxygen-containing compound” 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” and “cellular response to oxygen-containing compound” 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” and “cellular response to oxygen-containing compound” 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” and “cellular response to oxygen-containing compound” 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” and “cellular response to oxygen-containing compound” 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” and “cellular response to oxygen-containing compound” 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/D1ENTREZ GENE IDMEAN RATIO
CCNA24,8752665,3444551,9721330,0006500,0003660,0252151E+084,063951
PRDX32,1010212,1834251,8114950,0020890,0012950,0040911E+082,031980
MDM22,4368432,2327342,5619580,0001830,0002046,09E-051E+082,410512
FAS4,2082133,5066625,5369410,0001310,0001672,24E-053968264,417272
TPM13,1096783,8248993,6533850,0005820,0001830,0001551E+083,529321
CST33,6324185,3355896,5565420,0033050,0007250,0002867336725,174850
CDK14,8099453,890205-2,4356340,0000740,0001000,0006201E+082,088172
ARG14,3473051,136755-1,3355090,0008690,6986830,3108321,01E+081,382850
eISSN:
2544-3577
Language:
English
Publication timeframe:
4 times per year
Journal Subjects:
Life Sciences, Molecular Biology, Biochemistry
Journal RSS Feed