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. 2019 Sep 12;68(9):1515–1526. doi: 10.1007/s00262-019-02385-x

Table 2.

Gene expression and ontology enrichment in LCK-high samples

Top Over Expressed Genes
Symbol Name LCK non-high (geometric mean of intensities) LCK high (geometric mean of intensities) Fold changea Parametric p value FDR
 CXCL9 Chemokine (C–X–C motif) ligand 9 55.65 870.35 15.640 < 1e−07 < 1e−07
 IGLC1 Immunoglobulin lambda constant 1 (Mcg marker) 186.45 1984.25 10.642 < 1e−07 < 1e−07
 IGHM Immunoglobulin heavy constant mu 26.53 221 8.330 < 1e−07 < 1e−07
 IGKC Immunoglobulin kappa constant 26.11 226.8 8.686 < 1e−07 < 1e−07
 JCHAIN Joining chain of multimeric IgA and IgM 25.76 217.56 8.446 < 1e−07 < 1e−07
 IGKC Immunoglobulin kappa constant 27.05 221.33 8.182 < 1e−07 < 1e−07
 CXCL13 Chemokine (C–X–C motif) ligand 13 18.99 151.74 7.991 < 1e−07 < 1e−07
 IGHM Immunoglobulin heavy constant mu 16.18 113.07 6.988 < 1e−07 < 1e−07
 TRBC1 T cell receptor beta constant 1 32.03 208.74 6.517 < 1e−07 < 1e−07
 IGLJ3 Immunoglobulin lambda joining 3 23.3 154.25 6.620 < 1e−07 < 1e−07
 IGKC Immunoglobulin kappa constant 103.1 681.32 6.608 < 1e−07 < 1e−07
 CCL5 Chemokine (C–C motif) ligand 5 27.65 175.54 6.349 < 1e−07 < 1e−07
 TRBC1 T cell receptor beta constant 1 31.07 187.03 6.020 < 1e−07 < 1e−07
 IGLC1 Immunoglobulin lambda constant 1 (Mcg marker) 19.22 109.64 5.704 < 1e−07 < 1e−07
 CD2 CD2 molecule 24.16 129.36 5.354 < 1e−07 < 1e−07
 IGLJ3 Immunoglobulin lambda joining 3 13.85 71.54 5.165 < 1e−07 < 1e−07
 CD8A CD8a molecule 16.17 82.27 5.088 < 1e−07 < 1e−e−07
 CD3D CD3d molecule, delta (CD3-TCR complex) 34.53 175.11 5.071 < 1e−07 < 1e−07
 IGLV1-44 Immunoglobulin lambda variable 1-44 14.17 72.32 5.104 < 1e−07 < 1e−07
 GZMA Granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3) 10.61 51.3 4.835 < 1e−07 < 1e−07
 PTPRC Protein tyrosine phosphatase, receptor type, C 36.38 174.69 4.802 < 1e−07 < 1e−07
 IGHD Immunoglobulin heavy constant delta 19.21 91.97 4.788 < 1e−07 < 1e−04
 ADAMDEC1 ADAM-like, decysin 1 27.37 128.21 4.684 < 1e−07 < 1e−07
 IGLC1 Immunoglobulin lambda constant 1 (Mcg marker) 31.94 150.02 4.697 < 1e−07 < 1e−07
 LYZ Lysozyme 228.58 1099.09 4.808 < 1e−07 < 1e−07
 TRAC T cell receptor alpha constant 24.9 111.08 4.461 < 1e−07 < 1e−07
 HLA-DQB1 Major histocompatibility complex, class II, DQ beta 1 156.2 697.99 4.469 < 1e−07 < 1e−07
 GZMB Granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1) 17.16 74.13 4.320 < 1e−07 < 1e−07
 IGLJ3 Immunoglobulin lambda joining 3 14.66 62.9 4.291 < 1e−07 < 1e−07
 IDO1 Indoleamine 2,3-dioxygenase 1 37.75 163.3 4.326 < 1e−07 < 1e−07
 CXCL11 Chemokine (C–X–C motif) ligand 11 32.26 139 4.309 < 1e−07 < 1e−07
 CCL5 Chemokine (C–C motif) ligand 5 49.09 207.14 4.220 < 1e−07 < 1e−07
 CXCL11 Chemokine (C–X–C motif) ligand 11 21.48 90.56 4.216 < 1e−07 < 1e−07
 CXCL10 Chemokine (C–X–C motif) ligand 10 393.84 1622.47 4.120 2.74E−05 < 1e−07
 CD52 CD52 molecule 50.02 203.76 4.074 < 1e−07 < 1e−07
 PTPRC Protein tyrosine phosphatase, receptor type, C 74.72 304.33 4.073 < 1e−07 < 1e−07
 HLA-DQB1 Major histocompatibility complex, class II, DQ beta 1 87.61 351.26 4.009 < 1e−07 < 1e−07
Gene Ontology
GO ID GO term Observed in selected subset Expected in selected subset Observed/expectedb
 Cellular component
  GO:0042571 Immunoglobulin complex, circulating 7 0.15 46.41
  GO:0019814 Immunoglobulin complex 7 0.22 32.48
  GO:0042612 MHC class I protein complex 6 0.26 23.2
  GO:0061702 z complex 6 0.3 19.89
  GO:0042101 T cell receptor complex 6 0.39 15.47
 Molecular function
  GO:0032395 MHC class II receptor activity 7 0.17 41.73
  GO:0019957 C–C chemokine binding 5 0.17 29.8
  GO:0046977 TAP binding 6 0.22 26.82
  GO:0019865 Immunoglobulin binding 6 0.24 24.76
  GO:0004950 Chemokine receptor activity 8 0.34 23.84
  GO:0001637 G-protein coupled chemoattractant receptor activity 8 0.34 23.84
  GO:0023026 MHC class II protein complex binding 6 0.26 22.99
  GO:0019956 Chemokine binding 6 0.28 21.46
  GO:0045236 CXCR chemokine receptor binding 6 0.3 20.12
  GO:0023023 MHC protein complex binding 6 0.3 20.12
 Biological process
  GO:0002399 MHC class II protein complex assembly 5 0.15 32.44
  GO:0046113 Nucleobase catabolic process 5 0.18 27.8
  GO:0002396 MHC protein complex assembly 5 0.18 27.8
  GO:0010818 T cell chemotaxis 9 0.39 23.35
  GO:0002480 Antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent 5 0.23 21.62
  GO:0090026 Positive regulation of monocyte chemotaxis 7 0.36 19.46
  GO:0010819 Regulation of T cell chemotaxis 5 0.26 19.46
  GO:1901623 Regulation of lymphocyte chemotaxis 9 0.49 18.44
  GO:0036037 CD8-positive, alpha–beta T cell activation 5 0.31 16.22

aFold change < 4.0 are not reported

bObserved/expected < 15.0 not reported