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. 2007 Sep-Oct;13(9-10):495–508. doi: 10.2119/2007-00065.Shanley

Table 4A.

Gene Networks Downregulated Uniquely on Day One

Network and Central Node1 Ingenuity Annotations2 Panther Classifications3

  • Pathway (P value)

  • Biological Process (P value)

  • Molecular Function (P value)

 D.A.V.I.D. Functional Annotation4

  • Category

  • Term

  • P value
Network 1 BCL25

  • Hematologic system development

  • Immune system development

  • Lymphatic system development

  • T cell activation (2.2E-12)

  • T cell mediated immunity (7.4E-14)

  • Immunoglobulin receptor family member (1.9E-10)

  • SP_PIR_KEYWORDS

  • T cell

  • 1.4E-16
Network 2 HLA6

  • RNA posttranscriptional modification

  • Cell-cell signaling

  • Immune response

  • T cell activation (4.0E-7)

  • MHCII-mediated immunity (6.9E-19)

  • MHC antigen (2.0E-15)

  • KEGG_PATHWAY

  • Antigen processing and presentation

  • 2.2E-12
Network 3 TCF3

  • Hematologic system development

  • Immune system development

  • Lymphatic system development

  • Wnt signaling pathway (1.2E-2)

  • mRNA transcription regulation (3.2E-8)

  • Other transcription factor (1.1E-5)

  • GOTERM_BP_ALL

  • Regulation of cellular process

  • 3.9E-9
1

See Table 3A. BCL2, B-cell CLL/lymphoma 2; HLA, major histocompatibility complex; TCF3, transcription factor 3.

2,3,4

See Table 3A.

5

There is also a downregulated network on day three (see Table 4B) having BCL2 as the central node. Six of the 35 focus genes (17 percent) are different between the day one and the day three BCL2-related networks.

6

This network contains multiple HLA genes (HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DQA1, HLA-DQB1, HLA-DRA, and HLA-DRB1). There is also a downregulated network on day three that contains all of these HLA genes except for HLA-DMA and HLA-DRA. Overall, 13 of the 35 focus genes (37 percent) are different between the day one and the day three HLA-related networks.