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New markers of human cumulus oophorus cells cultured in vitro – transcriptomic profile

Maciej Brązert
Maciej Brązert
, 
Wiesława Kranc
Wiesława Kranc
, 
Karol Jopek
Karol Jopek
, 
Bartosz Kempisty
Bartosz Kempisty
 and 
Leszek Pawelczyk
Leszek Pawelczyk
   | Apr 29, 2020
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Published Online: Apr 29, 2020
Page range: 60 - 72
Received: Feb 25, 2020
Accepted: Apr 03, 2020
DOI: https://doi.org/10.2478/acb-2020-0007
Keywords
© 2020 Maciej Brązert, Wiesława Kranc, Karol Jopek, Bartosz Kempisty, Leszek Pawelczyk, published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

Heatmaps presenting differentially expressed genes involved in “cell junction organization”, “cell migration”, “cell morphogenesis involved in differentiation”, “cell morphogenesis” and “cell motility” based on GO BP terms. Each row on the Y axis represents a single transcript. The red color indicates downregulated genes while the green are upregulated
Heatmaps presenting differentially expressed genes involved in “cell junction organization”, “cell migration”, “cell morphogenesis involved in differentiation”, “cell morphogenesis” and “cell motility” based on GO BP terms. Each row on the Y axis represents a single transcript. The red color indicates downregulated genes while the green are upregulated

Figure 2

The circular scatter plots of differentially expressed genes involved in “cell junction organization”, “cell migration”, “cell morphogenesis involved in differentiation”, “cell morphogenesis” and “cell motility” GO BP terms. Each dot represents a single gene. The z-scores were presented as segments of inner circles
The circular scatter plots of differentially expressed genes involved in “cell junction organization”, “cell migration”, “cell morphogenesis involved in differentiation”, “cell morphogenesis” and “cell motility” GO BP terms. Each dot represents a single gene. The z-scores were presented as segments of inner circles

Figure 3

The dendrogram of differentially expressed genes involved in “cell junction organization”, “cell migration”, “cell morphogenesis involved in differentiation”, “cell morphogenesis” and “cell motility” GO BP terms. The DEGs were clustered based on their logFC values
The dendrogram of differentially expressed genes involved in “cell junction organization”, “cell migration”, “cell morphogenesis involved in differentiation”, “cell morphogenesis” and “cell motility” GO BP terms. The DEGs were clustered based on their logFC values

Figure 4

Analysis of enriched gene ontological groups involved in cellular morphogenesis, junction and migration. The network plot presenting the linkages of genes and GO BP terms
Analysis of enriched gene ontological groups involved in cellular morphogenesis, junction and migration. The network plot presenting the linkages of genes and GO BP terms

Figure 5

Heatmap presenting the relationship between genes and selected GO BP terms. The yellow color of tiles indicates the absence of logFC values
Heatmap presenting the relationship between genes and selected GO BP terms. The yellow color of tiles indicates the absence of logFC values

Figure 6

Interaction network of proteins encoded by 50 most changed DEGs belonging to “cell junction organization”, “cell migration”, “cell morphogenesis involved in differentiation”, “cell morphogenesis” and “cell motility” GO BP terms. The network was generated by STRING software. Network nodes represent proteins. Empty nodes indicate proteins of unknown 3D structure
Interaction network of proteins encoded by 50 most changed DEGs belonging to “cell junction organization”, “cell migration”, “cell morphogenesis involved in differentiation”, “cell morphogenesis” and “cell motility” GO BP terms. The network was generated by STRING software. Network nodes represent proteins. Empty nodes indicate proteins of unknown 3D structure

Figure 7

Reactome FI network for “Cell migration”. “--->” indicates activating/catalyzing, “-“ FIs extracted from complexes or inputs and “---” predicted FIs
Reactome FI network for “Cell migration”. “--->” indicates activating/catalyzing, “-“ FIs extracted from complexes or inputs and “---” predicted FIs

Figure 8

Reactome FI network for “Positive regulation of cell migration”. “--->” indicates activating/catalyzing, “-“ FIs extracted from complexes or inputs and “---” predicted FIs
Reactome FI network for “Positive regulation of cell migration”. “--->” indicates activating/catalyzing, “-“ FIs extracted from complexes or inputs and “---” predicted FIs

The 10 most significantly upregulated and all of the downregulated genes involved cellular morphogenesis, junction and migration

Gene symbolGene nameFold changeAdj.p.val
DKK1dicKKopf WNT signaling pathway inhibitor 134.81<0.05
ANXA3annexin A334.27<0.05
KIAA119SKIAA119927.73<0.05
VCAM1vascular cell adhesion molecule 126.69<0.05
HTR2B5-hydroxytryptamine (serotonin] receptor 2B, G protein-coupled24.33<0.05
CTGFconnective tissue growth factor18.97<0.05
TQFBR2transforming growth factor, beta receptor II (70/30l<Da)15.71<0.05
STC1stanniocalcin 114.96<0.05
CD74CD74 molecule, major histocompatibility complex, class II invariant chain14.18<0.05
SEMA5Asema domain, seven thrornbcsponüin repeats (type 1 arid type Hike), transrnembrane domain [TM) and short cytoplasriic domain, (semaphorin}5A13.15<0.05
SLC7A8solute carrier family 7 (amino acid transporter light chain, L system], member 9-2.00<0.05
DFNB31deafness, autosomal recessive 31-2.01<0.05
COL1A1collagen, type I, alpha 1-2.03<0.05
CDC42SE1CDC42 small effector 1-2.04<0.05
TSFBR3transforming growth factor, beta receptor III-2.05<0.05
HMGB1higri mobility group box 1-2.05<0.05
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