Overlaying of Core Network 3

As can be seen in Table 29, Core Network 3 was generated having 26 molecules from the dataset of All Top Regulated Genes and miRNAs being placed into a network of 70 molecules. The top diseases and functions found to be associated with molecules in Core Network 3 were cellular function and maintenance, cellular development, and haematological system development and function.

Figure 41 is overlaid with the dataset containing all the curated genes and miRNAs. A total of 35 genes and one miRNAs were mapped onto Core Network 3 above. Most of the genes mapped from this dataset lay on the periphery of the network. Of the 36 identifiers overlaid on this core network, only TRAF6, and miR-146a-5p appeared from this dataset to be a nodal gene and miRNA, respectively.

Figure 41: Core Network 3 overlaid with Starting Genes and miRNAs. Of the 866 Starting Genes and miRNAs mapped in IPA, 56 IDs were found in Core Network 3, composed of 216 molecules

138

Figure 42 shows Core Network 3 overlaid with all the genes and miRNAs found to interact with the set of curated genes and miRNAs, showing an association with lupus pathogenesis. The distribution of the overlay is widespread across the network. However, it is interesting to note that three genes, IRF5, IRF8, and IRF9, are not overlaid by the interactions dataset. These three genes were however, overlaid by the starting genes and miRNAs dataset in Figure 41. Thus, these three genes are considered in recent literature, or reported in the meta-analysis, to be associated with SLE, but these three genes were according to the analysis of miRTarBase, and miRecords, not found to be regulated by any of the curated lupus-associated miRNAs. Most of the genes from the overlay dataset of interacting genes and miRNAs are shown to be interacting with nodal genes (outlined by a red box), which were not found in miRTarBase or miRecords, to interact with any of the known lupus-associated miRNAs.

Figure 42: Core Network 3 overlaid with Interacting Genes and miRNAs. Of the 2969 Interacting Genes and miRNAs mapped in IPA, 164 IDs were found in Core Network 3, composed of 216 molecules

139

Figure 43 is overlaid with the dataset of all the miRNAs regulating 10 or more genes. Of the 32 identifiers overlaid, 31 were genes, and only one top regulating miRNA appeared in this network. The miRNA, miR-146a-5p, appeared in both the overlays for the starting, and the interacting datasets, see Figure 41 and Figure 42, respectively. This miRNA also appears as a nodal miRNA, and the only nodal gene overlaid in Figure 43 is TRAF6 (both outlined by a red box).

Figure 43: Core Network 3 overlaid with All Top Regulating miRNAs and associated genes. Of the 116 All Top Regulating miRNAs, and associated gene targets mapped in IPA, 32 IDs were found in Core Network 3, composed of 216 molecules

140

Figure 44 shows the result of overlaying the dataset containing all genes regulated by ten or more miRNAs. Four genes and one miRNA from this dataset appeared in Core Network 3. It is interesting to note that these five molecules all appeared in Figure 43, in which all the top regulated miRNAs and the genes they regulated were overlaid, unlike that seen in Core Networks 1, and 2, in which there was a noticeable difference between the two overlays, see Figure 31 and Figure 32, Figure 37 and Figure 38.

Figure 44: Core Network 3 overlaid with Top Regulated Genes and associated miRNAs. Of the 40 All Top Regulating genes, and associated miRNA targets mapped in IPA, 5 IDs were found in Core Network 3, composed of 216 molecules

141

Figure 45 is a result of Core Network 3 being overlaid with the complete dataset of all the top regulated genes and their associated miRNAs, and all the top regulating miRNAs and their association. Thus, Figure 45 is a combined overlay of both datasets used in Figure 43 and Figure 44. Figure 45 thus shows that of the top regulators and their interactions, most of the molecules are widespread across the network, and few form nodes. Most molecules can be found at the periphery of nodal interactions.

Figure 45: Core Network 3 overlaid with All Top Regulated Genes and miRNAs and associations. Of the 156 All Top Regulating Genes and miRNAs, and associated targets mapped in IPA, 32 IDs were found in Core Network 3, composed of 216 molecules.

142

Figure 46 was generated by first overlaying Core Network 3 with the complete list of starting, and interacting genes and miRNAs. Those molecules which were not overlaid were then manually selected and highlighted in pink.

Of the 31 molecules highlighted in pink, seven genes were identified as nodal genes (all outlined by an orange box), which were not present in the curated genes and miRNAs list, or the interactions list derived from miRTarBase, and miRecords. These six genes were: TFF1, RBBP4, IRF4, HSF1, GRB2, KHDRBS1, and IL1R1.

It is important to note that SMARCA4 (outlined by a blue box), is a gene overlaid only in Figure 42, yet it appears as an important node, interacting with numerous genes from the complete dataset of all curated and interaction data, as well as with new genes added by IPA.

Figure 46: Core Network 3 overlaid with All Genes and miRNAs, IPA added molecules in Pink. Of the 3687 All Genes and miRNAs, and associated targets mapped in IPA, 31 IDs were not overlaid in Core Network 3, and thus allowed for the identification of the molecules added in by IPA to complete the network structure.

143

11.12. Identification of candidate SLE-associated genes from