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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod165

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod165 Module size 49 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 696 BTN1A1 butyrophilin subfamily 1 member A1 11120 BTN2A1 butyrophilin subfamily 2 member A1 10385 BTN2A2 butyrophilin subfamily 2 member A2 11119 BTN3A1 butyrophilin subfamily 3 member A1 10384 BTN3A3 butyrophilin subfamily 3 member A3 56244 BTNL2 butyrophilin like 2 153579 BTNL9 butyrophilin like 9 23705 CADM1 cell adhesion molecule 1 253559 CADM2 cell adhesion molecule 2 57863 CADM3 cell adhesion molecule 3 199731 CADM4 cell adhesion molecule 4 9398 CD101 CD101 molecule 10666 CD226 CD226 molecule 80381 CD276 CD276 molecule 10225 CD96 CD96 molecule 94115 CGB8 chorionic gonadotropin subunit beta 8 56253 CRTAM cytotoxic and regulatory T cell molecule 79368 FCRL2 Fc receptor like 2 83416 FCRL5 Fc receptor like 5 152404 IGSF11 immunoglobulin superfamily member 11 22914 KLRK1 killer cell lectin like receptor K1 84569 LYZL1 lysozyme like 1 119180 LYZL2 lysozyme like 2 131375 LYZL4 lysozyme like 4 161357 MDGA2 MAM domain containing glycosylphosphatidylinositol anchor 2 5817 PVR poliovirus receptor 5818 PVRL1 nectin cell adhesion molecule 1 5819 PVRL2 nectin cell adhesion molecule 2 25945 PVRL3 nectin cell adhesion molecule 3 81607 PVRL4 nectin cell adhesion molecule 4 135250 RAET1E retinoic acid early transcript 1E 89790 SIGLEC10 sialic acid binding Ig like lectin 10 114132 SIGLEC11 sialic acid binding Ig like lectin 11 89858 SIGLEC12 sialic acid binding Ig like lectin 12 (gene/pseudogene) 100049587 SIGLEC14 sialic acid binding Ig like lectin 14 284266 SIGLEC15 sialic acid binding Ig like lectin 15 946 SIGLEC6 sialic acid binding Ig like lectin 6 27036 SIGLEC7 sialic acid binding Ig like lectin 7 27181 SIGLEC8 sialic acid binding Ig like lectin 8 27180 SIGLEC9 sialic acid binding Ig like lectin 9 140885 SIRPA signal regulatory protein alpha 10326 SIRPB1 signal regulatory protein beta 1 55423 SIRPG signal regulatory protein gamma 55080 TAPBPL TAP binding protein like 201633 TIGIT T cell immunoreceptor with Ig and ITIM domains 91937 TIMD4 T cell immunoglobulin and mucin domain containing 4 80329 ULBP1 UL16 binding protein 1 340547 VSIG1 V-set and immunoglobulin domain containing 1 23584 VSIG2 V-set and immunoglobulin domain containing 2

Functional annotation

Modules were tested for enrichment in functional and pathway annotations using two complementary approaches:
1. To select a small number of specific / non-redundant annotations for each module, a regression-based approach was used;
2. To obtain the complete set of enriched annotations, an extension of Fisher’s exact test that takes annotation bias into account was employed (Wallenius’ non-central hypergeometric distribution).

Most specific annotations for this module

Coeff.1 P-value.2 Source.3 Term.4 Class.5 3.98e-01 1.38e-16 Reactome Butyrophilin (BTN) family interactions Immune System 1.31e-01 2.43e-12 GO positive regulation of natural killer cell mediated cytotoxicity biological_process 1.21e-01 3.76e-07 Reactome Nectin/Necl trans heterodimerization Cell-Cell communication 6.91e-02 1.11e-08 GO susceptibility to natural killer cell mediated cytotoxicity biological_process 5.68e-02 3.05e-06 GO positive regulation of cell-cell adhesion biological_process 5.52e-02 3.05e-06 Reactome Signal regulatory protein family interactions Cell-Cell communication 3.68e-02 1.76e-06 GO cell recognition biological_process 2.45e-02 5.29e-08 GO T cell mediated cytotoxicity biological_process 2.07e-02 7.20e-06 GO positive regulation of T cell activation biological_process 1.61e-02 1.98e-17 Reactome Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell Immune System 3.78e-03 2.02e-10 GO carbohydrate binding molecular_function

¹Regression coefficient

²Fisher’s exact test nominal P-value

³Annotation source (Reactome, GO biological process (BP), molecular function (MF) and cellular component (CC))

⁴GO category or Reactome pathway

⁵High-level branch of annotation tree

Gene membership

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 0.00e+00 0.00e+00 regulation of natural killer cell mediated immunity 0.00e+00 0.00e+00 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules 0.00e+00 0.00e+00 cell-cell adherens junction 4.00e-12 3.65e-09 cell recognition 1.96e-11 1.74e-08 positive regulation of natural killer cell mediated cytotoxicity 2.12e-11 1.87e-08 positive regulation of natural killer cell mediated immunity 2.58e-11 2.26e-08 regulation of natural killer cell mediated cytotoxicity 5.84e-11 4.97e-08 positive regulation of leukocyte mediated cytotoxicity 6.30e-11 5.34e-08 homophilic cell adhesion via plasma membrane adhesion molecules 7.13e-11 3.75e-08 adherens junction 9.44e-11 7.86e-08 regulation of leukocyte mediated cytotoxicity 6.20e-10 4.74e-07 cell-cell adhesion via plasma-membrane adhesion molecules 4.59e-09 2.20e-06 carbohydrate binding 2.01e-08 8.74e-06 cell adhesion molecule binding 2.57e-08 9.66e-06 cell-cell junction 2.59e-08 1.11e-05 protein homodimerization activity 3.91e-08 2.35e-05 positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target 3.91e-08 2.35e-05 activated T cell proliferation 4.62e-08 2.75e-05 positive regulation of immune response to tumor cell 7.21e-08 4.17e-05 regulation of cytokine production

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 CELL CELL COMMUNICATION 0.00e+00 0.00e+00 IMMUNOREGULATORY INTERACTIONS BETWEEN A LYMPHOID AND A NON LYMPHOID CELL 0.00e+00 0.00e+00 ADHERENS JUNCTIONS INTERACTIONS 0.00e+00 0.00e+00 CELL CELL COMMUNICATION 1.46e-11 5.59e-09 CELL CELL JUNCTION ORGANIZATION 8.45e-11 3.08e-08 CELL JUNCTION ORGANIZATION 8.71e-11 2.40e-08 ADHERENS JUNCTIONS INTERACTIONS 2.09e-10 5.51e-08 IMMUNOREGULATORY INTERACTIONS BETWEEN A LYMPHOID AND A NON LYMPHOID CELL 2.63e-08 5.52e-06 CELL CELL JUNCTION ORGANIZATION 6.18e-08 1.23e-05 CELL JUNCTION ORGANIZATION 1.58e-06 2.66e-04 SIGNAL REGULATORY PROTEIN SIRP FAMILY INTERACTIONS 1.92e-06 4.11e-04 SIGNAL REGULATORY PROTEIN SIRP FAMILY INTERACTIONS 7.14e-03 6.10e-01 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 1.42e-02 1.00e+00 GLYCOPROTEIN HORMONES 1.59e-02 1.00e+00 PEPTIDE HORMONE BIOSYNTHESIS 1.72e-02 1.00e+00 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 2.70e-02 1.00e+00 PEPTIDE HORMONE BIOSYNTHESIS 2.70e-02 1.00e+00 GLYCOPROTEIN HORMONES

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 9.70e-05 2.22e-01 abnormal ciliary body morphology 1.89e-04 3.36e-01 abnormal anterior eye segment morphology 2.03e-04 3.52e-01 abnormal incisor color 2.24e-04 3.74e-01 abnormal vitreous body morphology 8.99e-04 8.46e-01 abnormal retinal layer morphology 1.20e-03 1.00e+00 increased T cell proliferation 2.65e-03 1.00e+00 abnormal incisor morphology 3.44e-03 1.00e+00 increased susceptibility to experimental autoimmune encephalomyelitis 3.75e-03 1.00e+00 increased pancreatic beta cell mass 3.75e-03 1.00e+00 increased pancreatic beta cell proliferation 4.32e-03 1.00e+00 abnormal macrophage physiology 6.41e-03 1.00e+00 abnormal T-helper 1 physiology 7.47e-03 1.00e+00 abnormal enamel rod pattern 7.48e-03 1.00e+00 small molars 7.91e-03 1.00e+00 abnormal lens morphology 9.33e-03 1.00e+00 abnormal testis weight 9.34e-03 1.00e+00 synostosis 9.34e-03 1.00e+00 abnormal plasma cell differentiation 1.24e-02 1.00e+00 increased interferon-gamma secretion 1.29e-02 1.00e+00 microphthalmia

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)