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The processes of homeostasis, chemotaxis and organic and inorganic response are significantly up-regulated during short-term oral mucosal cells in vitro cultivation

Blanka Borowiec
Blanka Borowiec
, 
Sylwia Ciesiółka
Sylwia Ciesiółka
, 
Krzysztof Janowicz
Krzysztof Janowicz
, 
Piotr Celichowski
Piotr Celichowski
, 
Artur Bryja
Artur Bryja
, 
Lisa Moncrieff
Lisa Moncrieff
, 
Greg Hutchings
Greg Hutchings
, 
Claudia Dompe
Claudia Dompe
, 
Bartosz Kempisty
Bartosz Kempisty
, 
Jamil A. Shibli
Jamil A. Shibli
, 
Paul Mozdziak
Paul Mozdziak
, 
Karolina Gerreth
Karolina Gerreth
 and 
Marta Dyszkiewicz-Konwińska
Marta Dyszkiewicz-Konwińska
   | Apr 29, 2020
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Published Online: Apr 29, 2020
Page range: 50 - 59
Received: Mar 03, 2020
Accepted: Apr 06, 2020
DOI: https://doi.org/10.2478/acb-2020-0006
Keywords
© 2020 Blanka Borowiec, Sylwia Ciesiółka, Krzysztof Janowicz, Piotr Celichowski, Artur Bryja, Lisa Moncrieff, Greg Hutchings, Claudia Dompe, Bartosz Kempisty, Jamil A. Shibli, Paul Mozdziak, Karolina Gerreth, Marta Dyszkiewicz-Konwińska,, 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 divalent inorganic cation homeostasis”, “chemical homeostasis”, “chemotaxis”, “homeostatic process” and “response to organic substance” 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 “cellular divalent inorganic cation homeostasis”, “chemical homeostasis”, “chemotaxis”, “homeostatic process” and “response to organic substance” 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 “cellular divalent inorganic cation homeostasis”, “chemical homeostasis”, “chemotaxis”, “homeostatic process” and “response to organic substance” 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 divalent inorganic cation homeostasis”, “chemical homeostasis”, “chemotaxis”, “homeostatic process” and “response to organic substance” 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 “cellular divalent inorganic cation homeostasis”, “chemical homeostasis”, “chemotaxis”, “homeostatic process” and “response to organic substance” GO BP terms. The ribbons indicate which gene belongs to which categories. The middle circle represents logarithm from fold change (LogFC) between D15/D7, D30/D7 and D30/D15 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 “cellular divalent inorganic cation homeostasis”, “chemical homeostasis”, “chemotaxis”, “homeostatic process” and “response to organic substance” GO BP terms. The ribbons indicate which gene belongs to which categories. The middle circle represents logarithm from fold change (LogFC) between D15/D7, D30/D7 and D30/D15 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 genes that belongs to 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 genes that belongs to 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 differently expressed genes that belongs to the “cellular divalent inorganic cation homeostasis”, “chemical homeostasis”, “chemotaxis”, “homeostatic process” and “response to organic substance” GO BP terms. The intensity of the edges reflects the interaction. The explanation of each symbol is included on the legend included in figure
STRING-generated interaction occurrence differently expressed genes that belongs to the “cellular divalent inorganic cation homeostasis”, “chemical homeostasis”, “chemotaxis”, “homeostatic process” and “response to organic substance” GO BP terms. The intensity of the edges reflects the interaction. The explanation of each symbol is included on the legend included in figure

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

GENE SYMBOLGENE IDRATIO D7/D15RATIO D7/D30P VAL D7/D15P VAL D7/D30MEAN RATIO
SPP1397087-10.87016565-14.25386170.0162712040.023019379-12.56201368
CCL8100302703-9.10436286-9.8466712980.0099091620.002855033-9.475517079
CXCL2414904-6.305216475-2.7637651870.0282105710.100060673-4.534490831
PTGS2397590-5.663189033-3.050664860.0332721530.086182814-4.356926947
ATP13A3100522900-3.576872002-3.4272047350.0338445670.040686213-3.502038369
PPARD397671-2.416675019-4.0053911160.0520060620.023501509-3.211033067
ATP1B1396898-3.743863827-2.0104473740.0311184930.123030328-2.8771556
CCL2397422-3.929361381-1.4507799290.0407438210.404390916-2.690070655
LYN100152890-2.52053573-2.4545351960.0346364920.04233411-2.487535463
REL100525104-3.00471739-1.965554050.0234279480.05637387-2.48513572
FCER1G397406-2.351156762-2.4045880580.0268356760.023565415-2.37787241
ETS1100302363-2.513407982-2.1505219830.0311184930.047472133-2.331964982
SCARB1397018-2.623056585-1.6817499410.0346364920.134327075-2.152403263
STEAP1397573-2.349620022-1.886629360.0268356760.044202404-2.118124691
ITGB3397063-2.917250333-1.3110252150.0388980030.421388587-2.114137774
IL6399500-1.793617663-2.2493345650.0884647660.044202404-2.021476114
LMO2100512825-2.0687671-1.8563698050.0268356760.034894667-1.962568452
TGFB1397078-2.253272341-1.2263169220.0150164240.216600729-1.739794631
CEBPA397307-1.147965724-2.1750530030.3207822940.017618993-1.661509363
DMD497636-1.6036745931.6312092280.0724618040.0681616960.013767318
LGALS9396972-1.5727100662.9108823240.13986140.0235015090.669086129
ATP5B1001571561.1223311711.0732466630.4828867530.629795881.097788917
NPFFR2---1.0445702662.0100060040.8269962090.0267077711.527288135
OAS1---1.0233182222.2555192230.9115526380.0230193791.639418722
PIN11005128272.0226942061.5818520960.042525030.1175935141.802273151
DKK36646531.7780400652.3626759080.04660370.0235015092.070357987
ATP6V1G21001523582.3468914121.830723960.0130320380.0235015092.088807686
TADA31001574642.5100731241.9779354590.0150164240.0249341842.244004291
MEF2C7335901.8012793553.2239186820.0811989980.0235015092.512599019
RUNX21007379652.6584564362.6662268730.042525030.0474721332.662341655
CD343971602.3630675013.0933632560.0522913520.0348946672.728215378
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