Ontology and network analysis of genes at clustered integration sites. (A) Clustered integration sites at the LMO2 locus. The green and red lines indicate the position of vector integration sites. Forward indicates that the vector is oriented 5′ to 3′ relative to the chromosomal numbering system. Reverse indicates reverse orientation. The arrow indicates the direction of LMO2 transcription. Only selected splice variants are shown. Annotation similar in subsequent panels. (B) Clustered integration sites at the CCND2 locus. (C) Clustered integration sites at the SEPT9 locus. (D) Clustered integration sites at the JARID2 locus. (E) Clustered integration sites at the NOTCH2 locus. (F) Gene classes enriched near integration sites. The x-axis shows the statistical significance for enriched groups as the negative log of P after correction for multiple comparisons (Benjamini). The number at the end of each bar indicates the number of genes near integration sites in each category (categories were defined by the DAVID gene ontology). The raw ontology output was edited to remove uninformative high level classes or duplicative annotation. (G) A regulatory network defined by genes at clustered integration sites. The network was generated using Ingenuity, which uses published literature on interactions or affinity screens to link genes (solid line indicates direct relationships, dashed line indicates indirect relationships, arrow indicates directionality of the relationship). All networks are shown that involved more than 2 genes. No attempt was made to assess statistical significance of this network.