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Biochemical properties of cofactor and coenzyme metabolism in porcine oviductal epithelial cells – a microarray study

Ievgeniia Kocherova
Ievgeniia Kocherova
, 
Magdalena Kulus
Magdalena Kulus
, 
Claudia Dompe
Claudia Dompe
, 
Paweł Antosik
Paweł Antosik
, 
Dorota Bukowska
Dorota Bukowska
, 
Bartosz Kempisty
Bartosz Kempisty
 e 
Paul Mozdziak
Paul Mozdziak
   | 08 nov 2019
Medical Journal of Cell Biology's Cover Image
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Pubblicato online: 08 nov 2019
Pagine: 125 - 133
Ricevuto: 11 set 2019
Accettato: 19 ott 2019
DOI: https://doi.org/10.2478/acb-2019-0017
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© 2019 Ievgeniia Kocherova, Magdalena Kulus, Claudia Dompe, Paweł Antosik, Dorota Bukowska, 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 to “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” 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)
Heat map representation of differentially expressed genes belonging to the to “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” 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)

Figure 2

The circle plot showing the differently expressed genes and z-score of the “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” 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 “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” 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 belong to “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” 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 – up-regulated, red – down-regulated). The genes were sorted by logFC from most to least changed gene
The representation of the mutual relationship of differently expressed genes that belong to “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” 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 – up-regulated, red – down-regulated). The genes were sorted by logFC from most to least changed gene

Figure 4

Heatmap showing the gene occurrence between chosen differently expressed genes that belongs to “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” 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 differently expressed genes that belongs to “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” 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 chosen differently expressed genes that belongs to the to “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. The intensity of the edges reflects the strength of interaction score
STRING-generated interaction occurrence between chosen differently expressed genes that belongs to the to “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. The intensity of the edges reflects the strength of interaction score

Figure 6

Functional interaction (FI) between chosen differently expressed genes that belongs to the to “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” 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 chosen differently expressed genes that belongs to the to “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” 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
ACSL42,078475-1,049840-1,3898650,0008880,7788470,027679448980-0,120410
HAAO2,2604621,012229-1,4845480,0004950,9482520,0109111005142830,596048
PPARA2,1567411,4636971,4317600,0016970,0364120,0404843972391,684066
CPOX2,5624601,5134751,3952390,0004900,0199460,0427251005114741,823725
ALDOC3,1005751,2154951,3173600,0003010,2745400,1104451005120131,877810
PGM12,4245191,6807561,6915670,0002760,0029240,0021533975661,932281
TPI12,7511771,7373871,4210650,0000590,0007790,0061331001575821,969876
ME12,6919751,5280671,9117220,0003580,0172060,0017233975382,043921
ACSL32,0495551,6769122,7299730,0020970,0086050,0002181002331692,152147
FECH2,1099182,7220322,4201940,0006780,0001170,0001521003228732,417382
SLC25A13,2722471,8576862,2390220,0000430,0006490,0001171001543102,456318
OXSM2,2344152,6970092,5143160,0005600,0001430,000144---2,481914
PFKFB42,9782453,6994732,5737600,0001320,0000340,0001221001580563,083826
PDK14,8564761,9814582,6582240,0001000,0044180,0005371002868713,165386
PCBD12,8312663,2346743,4362040,0000470,0000150,0000071001556053,167382
ACACA3,4117493,7300453,5013880,0005880,0003070,0002793973243,547727
TSPO3,1239063,9629453,6690100,0000480,0000120,0000093965923,585287
ACOT132,2037694,2645284,9689300,0002330,0000080,0000031005145873,812409
SCD5,0378821,4027675,7968470,0000920,0874830,0000253966704,079166
PDK32,7737704,0661515,4866280,0001820,0000240,0000061001538584,108850
AASS2,3329314,1192426,1324470,0073290,0004760,0000921005139624,194873
ACSS26,3497182,5033935,6209300,0000070,0000950,0000021001538664,824680
PANK17,8555623,4916747,1586500,0000070,0000330,0000021001546506,168629
P2RX76,1651428,5220425,7953980,0000270,0000070,0000104976236,827528
ALDH1L24,5357938,62634722,1027550,0000380,0000040,00000110015197611,754965
eISSN:
2544-3577
Lingua:
Inglese
Frequenza di pubblicazione:
4 volte all'anno
Argomenti della rivista:
Life Sciences, Molecular Biology, Biochemistry
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