Table II. Selected relevant genes hypoexpressed in DS thymus displayed by category and function
Gene SymbolGene ProductChromosomal LocationBiological Process (Module 1)Biological Process (Module 2)
KIF23Kinesin-like protein family15q23DNA metabolic process; mitosis; cell division; cell cycle, DNA repairMicrotubule-based process
ZWINTA protein involved in kinetochore function10q21-q22Chromosome organization; spindle organization, mitosis; cell division; cell cycle; chromosome segregation; etc.Microtubule-based process
GRAP2This gene encodes a member of the GRB2/Sem5/Drk family. This member is an adapter-like protein involved in leukocyte-specific protein-tyrosine kinase signaling.22q13.2Cell division, mitosis, Ras protein signal transduction, intracellular signaling cascade
PRDX2Peroxiredoxin family of antioxidant enzymes19p13.2Lymphocyte activation; cell proliferation; cell division; regulation of hydrogen peroxide metabolic process; thymus development; T cell differentiation; regulation of lymphocyte activation; homeostasis of number of cellsRegulation of T cell activation; immune response; negative regulation of T cell differentiation
PRSS16Serine protease expressed exclusively in the thymus6p21Nucleotide binding
IL2RGIL-2R, γXq13.1Lymphocyte activation; cell division; mitosis; interspecies interaction between organism; T cell activationRegulation of T cell activation; positive regulation of immune system process; immune response
RAG2This gene encodes a protein that is involved in the initiation of V(D)J recombination during B and T cell development11p3DNA metabolic process, cell proliferation, cell division, mitosis, T cell differentiation, DNA recombinationB cell homeostatic proliferation, immune response
SH2D1ARole in the bidirectional stimulation of T and B cellsXq25-q26MitosisPositive regulation of immune system process
CD3DPart of the TCR–CD3 complex11q23Lymphocyte activation, cell division, mitosis, T cell differentiationPositive thymic T cell selection, T cell selection
CD3ECD3-ε polypeptide11q23Cell proliferation; protein amino acid phosphorylation; lymphocyte activation; T cell differentiationNegative thymic T cell selection; T cell selection
HLA-DRB3HLA-DRB3 belongs to the HLA class II β-chain paralogs. This class II molecule is a heterodimer consisting of an α (DRA) and a β (DRB) chain, both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins.6p21.3MitosisImmune response, Ag processing and presentation
HLA-DQB1HLA-DQB1 belongs to the HLA class II β-chain paralogs6p21.3Cell division, mitosisAg processing and presentation of peptide or polysaccharide Ag via MHC class II, Ag processing and presentation
CD1ACD1 family of transmembrane glycoproteins1q22-q23Cell division, mitosisAg processing and presentation
CD1BCD1 family of transmembrane glycoproteins1q22-q23Cell divisionImmune response; Ag processing and presentation
CD1CCD1 family of transmembrane glycoproteins1q22-q23Mitosis; cell divisionImmune response; Ag processing and presentation
CD1DCD1 family of transmembrane glycoproteins1q22-q23Lymphocyte activation; mitosis; interspecies interaction between organisms; T cell differentiationAg processing and presentation of endogenous Ag; immune response; T cell selection; Ag processing and presentation
CD74CD74 molecule, MHC class II invariant chain5q32Mitosis, intracellular signaling cascade, protein amino acid phosphorylation, lymphocyte activation, cell proliferation, cell divisionAg processing and presentation of endogenous Ag, positive regulation of immune system process, positive regulation of immune system process, regulation of T cell activation, negative thymic T cell selection, immune response, positive thymic T cell selection, T cell selection
TOP2ATopoisomerase (DNA) II α. This gene is an AIRE partner and encodes a DNA topoisomerase that controls and alters the topologic states of DNA during transcription.17q21-q22DNA replication, intracellular signaling cascadePositive regulation of retroviral genome replication
LCKProtein tyrosine kinases1p34.3Protein amino acid phosphorylation; cell division; mitosis; positive regulation of TCR signaling pathway; interspecies interaction between organisms; TCR signaling pathwayPositive regulation of immune system process; regulation of T cell activation; immune response
LATLinker for activation of T cells16p11.2Lymphocyte activation; cell division; mitosis; RAS protein signal transduction; regulation of lymphocyte activation; intracellular signaling cascadeRegulation of T cell activation; immune response
ERAP2ERAP1 (MIM 606832) and LRAP to trim precursors to antigenic peptides in the endoplasmic reticulum5q15Cell division, mitosisAg processing and presentation of endogenous Ag, immune response
IKZF1Family zinc finger 17p13-p11.1T cell differentiation, regulation of lymphocyte activation, lymphocyte activationPositive regulation of immune system process, regulation of T cell activation
SLAMF1Signaling lymphocytic activation molecule family member 11q22-q23Interspecies interaction between organisms, lymphocyte activation, cell proliferation, cell division, mitosis
CXCR4CXCR specific for stromal cell-derived factor-12q21Mitosis, interspecies interaction between organisms, intracellular signaling cascade, cell divisionImmune response
CHEK1CHK1 checkpoint homolog (S. pombe)11q24-q24Cell proliferation, cell division, mitosis, meiosis, cell cycleMeiosis
FEN1DNA repair and processes the 5′ ends of Okazaki fragments in lagging strand DNA synthesis11q12Cell division, mitosis
CCNB2Cyclin family15q22.2Cell division, mitosis, cell cycle, thymus development
MLF1IPSpecialized chromatin domain4q35.1Mitosis, interspecies interaction between organisms, cell division
E2F7Plays an essential role in the regulation of cell cycle progression12q21.2Cell proliferation
  • —, Not present in Module 2.