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The genes regulating maintenance of cellular protein location are differentially expressed in porcine epithelial oviductal cells during longterm in vitro cultivation

Katarzyna Stefańska
Katarzyna Stefańska
, 
Ievgenia Kocherova
Ievgenia Kocherova
, 
Sandra Knap
Sandra Knap
, 
Magdalena Kulus
Magdalena Kulus
, 
Piotr Celichowski
Piotr Celichowski
 y 
Michal Jeseta
Michal Jeseta
   | 12 oct 2019
Medical Journal of Cell Biology's Cover Image
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Publicado en línea: 12 oct 2019
Páginas: 77 - 85
Recibido: 06 ago 2019
Aceptado: 13 sept 2019
DOI: https://doi.org/10.2478/acb-2019-0010
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© 2019 Katarzyna Stefańska, Ievgenia Kocherova, Sandra Knap, Magdalena Kulus, Piotr Celichowski, 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 to “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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 “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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 “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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 “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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 “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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 “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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 “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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 “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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 “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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 “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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 “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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 “maintenance of location”, maintenance of protein location in cell” and “ maintenance of protein location” 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
PLIN2-4,907-3,554-4,5931,11*10^51,34*10^53,34*10^6397402-4,352
UBASH3B-1,211-3,527-6,5412,19*10^15,65*10^54,84*10^6100521108-3,760
CHD7-2,636-3,935-4,4472,97*10^43,61*10^51,51*10^5100157083-3,673
DRD2-1,904-4,799-2,9461,12*10^31,05*10^54,14*10^5100624857-3,216
CXCL10-4,137-2,237-3,0152,16*10^32,59*10^24,92*10^3494019-3,130
NOS1-2,717-2,984-2,6792,24*10^49,95*10^51,15*10^4100520934-2,794
EZR-1,728-2,489-3,4041,74*10^31,06*10^41,49*10^5100152815-2,540
NFKBIA-2,378-2,256-2,4643,20*10^43,17*10^41,30*10^4406188-2,366
ANK3-1,644-2,184-3,0634,87*10^26,10*10^37,47*10^4100154687-2,297
F2R-2,545-2,149-2,1856,98*10^41,46*10^39,88*10^4100521609-2,293
ITGAV5,8156,5076,7381,26*10^46,01*10^53,42*10^53972856,353
C32,6658,3329,4366,56*10^41,06*10^54,89*10^63970726,811
P2RX76,1658,5225,7952,69*10^56,72*10^61,03*10^54976236,828
ABCA16,3135,55710,3363,95*10^53,12*10^54,36*10^61001521127,402
ANK23,0856,71915,9911,37*10^46,90*10^67,60*10^72878,598
HTR1B3,4849,04814,4521,32*10^45,34*10^61,26*10^63975638,994
BDKRB12,81817,59414,2461,32*10^41,36*10^65,99*10^710012746911,553
ITGB312,67413,16010,9354,27*10^61,55*10^68,03*10^739706312,256
FBN13,69227,54762,8491,51*10^41,63*10^63,07*10^741483631,363
THY138,75332,74331,3023,01*10^61,39*10^65,59*10^710027193134,266
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Life Sciences, Molecular Biology, Biochemistry
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