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Transcriptomic profile of genes encoding proteins responsible for regulation of cells differentiation and neurogenesis in vivo and in vitro – an oocyte model approach

Lisa Moncrieff
Lisa Moncrieff
, 
Ievgeniia Kocherova
Ievgeniia Kocherova
, 
Artur Bryja
Artur Bryja
, 
Wiesława Kranc
Wiesława Kranc
, 
Joanna Perek
Joanna Perek
, 
Magdalena Kulus
Magdalena Kulus
, 
Michal Jeseta
Michal Jeseta
, 
Claudia Dompe
Claudia Dompe
, 
Greg Hutchings
Greg Hutchings
, 
Krzysztof Janowicz
Krzysztof Janowicz
, 
Piotr Celichowski
Piotr Celichowski
, 
Małgorzata Bruska
Małgorzata Bruska
, 
Maciej Zabel
Maciej Zabel
, 
Bartosz Kempisty
Bartosz Kempisty
 e 
Paul Mozdziak
Paul Mozdziak
   | 29 apr 2020
Medical Journal of Cell Biology's Cover Image
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Pubblicato online: 29 apr 2020
Pagine: 1 - 11
Ricevuto: 19 dic 2019
Accettato: 05 feb 2020
DOI: https://doi.org/10.2478/acb-2020-0001
Parole chiave
© 2020 Lisa Moncrieff, Ievgeniia Kocherova, Artur Bryja, Wiesława Kranc, Joanna Perek, Magdalena Kulus, Michal Jeseta, Claudia Dompe, Greg Hutchings, Krzysztof Janowicz, Piotr Celichowski, Małgorzata Bruska, Maciej Zabel, 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 representations of differentially expressed genes belonging to the “neuron differentiation” and “negative regulation of cell differentiation” 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 representations of differentially expressed genes belonging to the “neuron differentiation” and “negative regulation of cell differentiation” 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 “neuron differentiation” and “negative regulation of cell differentiation” GO BP Terms. The outer circle shows a scatter plot for each term of the fold change of the assigned genes. Red circles display 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 “neuron differentiation” and “negative regulation of cell differentiation” GO BP Terms. The outer circle shows a scatter plot for each term of the fold change of the assigned genes. Red circles display 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 between differently expressed genes that belong to the “neuron differentiation” and “negative regulation of cell differentiation” GO BP Terms. The ribbons indicate which gene belongs to which categories. The middle circle represents logarithm from fold change (LogFC) between before IVM and after IVM respectively. The genes were sorted by logFC from most to least changed gene
The representation of the mutual relationship between differently expressed genes that belong to the “neuron differentiation” and “negative regulation of cell differentiation” GO BP Terms. The ribbons indicate which gene belongs to which categories. The middle circle represents logarithm from fold change (LogFC) between before IVM and after IVM respectively. The genes were sorted by logFC from most to least changed gene

Figure 4

Heatmap showing the gene occurrence between differently expressed genes that belongs to the “neuron differentiation” and “negative regulation of cell differentiation” GO BP Terms. The intensity of the color is corresponding to amount of GO BP terms that each gene belongs to
Heatmap showing the gene occurrence between differently expressed genes that belongs to the “neuron differentiation” and “negative regulation of cell differentiation” GO BP Terms. The intensity of the color is corresponding to amount of GO BP terms that each gene belongs to

Figure 5

STRING-generated interaction network between genes that belongs to the “neuron differentiation” and “negative regulation of cell differentiation” GO BP Terms. The intensity of the edges reflects the strength of interaction score
STRING-generated interaction network between genes that belongs to the “neuron differentiation” and “negative regulation of cell differentiation” GO BP Terms. The intensity of the edges reflects the strength of interaction score

Gene symbols, Entrez gene IDs, ratio and corrected P values of studied genes

GENE SYMBOLENTREZ GENE IDRATIOP VALUE
VEGFA397157-14.349386890.001912689
BTG2100048932-13.443318930.0000955
MCOLN3100625693-7.2037544510.000850265
EGR2100038004-6.0421561750.007949861
TGFBR3397512-5.0884824930.000405979
GJA1100518636-4.8330811470.000107676
FST445002-4.4504464490.000364693
CTNNA2100525337-4.3492396650.000512181
RTN4100170118-4.3219371180.027495815
MDGA1397529-4.2931840010.003493167
SLITRK3106504067-4.1816175060.004260951
INHBA397093-4.1449098490.000148036
CDK6100518921-4.0322350860.006042481
LAMB2101101688-3.5860552370.000187911
ROBO2100517681-3.5242431850.001183495
CUX1100521258-3.3420529210.000372663
IHH397174-3.2787332070.000551261
EMX2100152562-3.123877060.001929388
ZCCHC11100516979-3.1092371390.019809962
APP397663-3.085099970.005602323
WWTR1100522573-3.0562151750.000254025
SMARCA1100188905-3.0382116130.014758847
SEMA5A100737194-2.8297211190.001092396
ITGB1397019-2.730502040.003705215
SMAD4397142-2.718852680.001238681
RORA100156637-2.604679250.021553766
NOTCH2100153369-2.5985756680.002523723
RYK100523513-2.3702130230.00439989
KIT396810-2.3231814140.00255635
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Lingua:
Inglese
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Argomenti della rivista:
Life Sciences, Molecular Biology, Biochemistry
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