Fig 1.
Transcriptome analysis of calcium-induced differentiation of human primary epidermal stem cells.
(A) Experimental transcriptome analysis of the different process [3]. Differentiation was induced in human primary stem cells with 1.2mM CaCl2. Cells were collected every 5 hours in triplicates during 45 hours, total RNA was extracted from each sample, synthesized into cDNA, amplified in cRNA, Cy3 labeled, and hybridized to microarrays. Data were collected, normalized and gens were classified based on expression profiles. (B) Clusters of gene expression dynamics along differentiation. The 1317 expressed super-dynamic genes were clustered using K-means clustering and the proportion of the different functional categories is shown in the pie diagrams below. See also the legend.
Fig 2.
Paralog analysis of dynamic genes.
(A) Known example from literature for opposite expression changes of paralogs involved in gap junction permeability [29]. (B) Statistics for correlated and anti-correlated dynamic and super-dynamic proteins. There are 950 highly co-expressed (r> = 0.6) dynamic paralogous pairs, 235 of which are super-dynamic and 281 highly anti-correlated (r< = -0.6) dynamic paralogous pairs, 19 of which are super-dynamic. (C) Example for correlated pairs (super dynamic), grouped by paralogous families. (D), (E), and (F): example for anti-correlated (super dynamic) grouped according to paralogous families. (G) Pfam domain differences between dynamic paralogous pairs. 281 anti-correlated paralogs (r< = -0.6) have a mean of 1.7 differences compared to 950 correlated paralogs (r> = 0.6) which have a mean difference of 1.28 in their domains (P = 0.009). The statistical significance was tested using Wilcoxon rank sum test.
Fig 3.
Statistics of expression profiles mapped on human protein complexes.
(A) Statistic of protein complexes with subunits classified as non-dynamic, unresolved, dynamic, super-dynamic, or a combination of classes. When including unresolved genes in the non-dynamic class, 28% of the complexes are non-dynamic/unresolved, 18% are di-chromatic (63% if we include unresolved genes), and 9% are only dynamic/super-dynamic. (B) Excluding all complexes with any unresolved subunits results in 55% di-chromatic complexes, 19% completely non-dynamic, and 26% completely dynamic/super-dynamic.
Fig 4.
Network representation of human protein complexes with di-chromatic expression profiles.
Protein interaction network representation of human protein complexes containing at least one super-dynamic subunit. Dynamic genes were re-clustered based on best agreement with one of the eight super-dynamic clusters. The nodes are colored according to cluster membership (see Fig 5) and node sizes are indicative of fold absolute changes over time. The network is represented using Cytoscape.
Fig 5.
Selected di-chromatic complexes with cellular functions involved in keratinocyte differentiation.
(A) Schematic overview of cellular processes involved in keratinocyte differentiation. (B) Selected CORUM complexes of similar core proteins were plotted. Super-dynamic and dynamic genes were colored according to clusters. Black indicates constitutive genes, grey indicated unresolved genes.
Fig 6.
Combining expression classification with compatible (AND) and mutually exclusive (XOR) interaction types and summary of complex assembly motifs.
(A) Left panel, schematic representation of possible cases combining protein expression classification with surface interaction types: compatible (AND) and mutually exclusive (XOR) interactions. Discounting unresolved class, there are six possible cases, out of which three biologically meaningful ones were selected. Case 1: the hub protein is non-dynamically expressed while the attachment proteins are dynamic; case 2: all three interacting proteins are dynamic; and case 3: all three interacting proteins are non-dynamic. For the remaining cases, including unresolved genes, see S16 Fig Right panel shows percentages of protein interaction triplets analysed structurally by SAPIN for cases 1 to 3. Of protein triplets of case 1, 65% (n = 49) have XOR interactions compared to 35% (n = 27) AND, of case 2 61% (n = 128) have XOR interactions compared to 39% (n = 81) AND interactions and finally of case 3, 61% show AND interactions (n = 628) compared to 39% (n = 397) XOR. Statistical significance tested using Fisher test where * indicates p < 0.0001 and ** indicates p < 0.00001. Multiple testing correction was conducted with Bonferroni method resulting in all q < 0.005. For the remaining cases, including unresolved genes, see S19–S21 Figs (B) Summary of the complex assembly motifs proposed for the process of keratinocyte differentiation.