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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod293

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod293 Module size 27 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1 A1BG alpha-1-B glycoprotein 92747 BPIFB1 BPI fold containing family B member 1 338872 C1QTNF9 C1q and TNF related 9 387911 C1QTNF9B C1q and TNF related 9B 10584 COLEC10 collectin subfamily member 10 78989 COLEC11 collectin subfamily member 11 200407 CREG2 cellular repressor of E1A stimulated genes 2 167 CRISP1 cysteine rich secretory protein 1 7180 CRISP2 cysteine rich secretory protein 2 1755 DMBT1 deleted in malignant brain tumors 1 256710 GLIPR1L1 GLIPR1 like 1 55716 LMBR1L limb development membrane protein 1 like 8685 MARCO macrophage receptor with collagenous structure 131149 OTOL1 otolin 1 51050 PI15 peptidase inhibitor 15 140902 R3HDML R3H domain containing like 7356 SCGB1A1 secretoglobin family 1A member 1 92304 SCGB3A1 secretoglobin family 3A member 1 117156 SCGB3A2 secretoglobin family 3A member 2 653509 SFTPA1 surfactant protein A1 729238 SFTPA2 surfactant protein A2 6439 SFTPB surfactant protein B 6441 SFTPD surfactant protein D 11013 TMSB15A thymosin beta 15a 11013 TMSB15B thymosin beta 15a NA TMSB4XP4 9087 TMSB4Y thymosin beta 4 Y-linked

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 2.55e-01 1.87e-06 Reactome Defective SFTPA2 causes idiopathic pulmonary fibrosis (IPF) Disease 1.27e-01 4.36e-12 GO monosaccharide binding molecular_function 1.21e-01 2.86e-07 GO sequestering of actin monomers biological_process 8.78e-02 2.04e-10 Reactome Defective CSF2RA causes pulmonary surfactant metabolism dysfunction 4 (SMDP4) Disease 8.63e-02 2.04e-10 Reactome Defective CSF2RB causes pulmonary surfactant metabolism dysfunction 5 (SMDP5) Disease 4.48e-02 7.11e-17 GO collagen trimer cellular_component 3.10e-02 8.36e-05 GO peptidase inhibitor activity molecular_function 1.86e-02 2.29e-06 Reactome Scavenging by Class A Receptors Vesicle-mediated transport 7.37e-03 1.02e-04 GO signaling pattern recognition receptor activity molecular_function 5.54e-03 1.34e-07 GO lamellar body cellular_component

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 collagen trimer 6.66e-09 4.43e-06 pattern recognition receptor signaling pathway 7.70e-09 3.11e-06 endocytic vesicle 1.24e-08 4.84e-06 lamellar body 3.70e-08 2.23e-05 regulation of innate immune response 3.76e-08 2.26e-05 positive regulation of immune response 8.96e-08 5.10e-05 respiratory gaseous exchange 1.20e-07 6.70e-05 innate immune response-activating signal transduction 1.39e-07 4.61e-05 clathrin-coated endocytic vesicle 1.52e-07 8.32e-05 activation of innate immune response 2.92e-07 1.53e-04 positive regulation of innate immune response 5.96e-07 2.96e-04 endocytosis 1.75e-06 7.95e-04 immune response-activating signal transduction 3.21e-06 1.38e-03 immune response-regulating signaling pathway 3.30e-06 1.42e-03 receptor-mediated endocytosis 8.46e-06 2.24e-03 actin monomer binding 1.33e-05 3.19e-03 clathrin-coated vesicle 1.40e-05 5.23e-03 toll-like receptor signaling pathway 1.79e-05 6.52e-03 humoral immune response 2.69e-05 6.05e-03 secretory granule

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.63e-07 3.08e-03 abnormal surfactant physiology 3.28e-05 1.08e-01 abnormal surfactant composition 1.17e-04 2.50e-01 abnormal surfactant secretion 7.85e-04 7.82e-01 abnormal cytokine level 1.87e-03 1.00e+00 increased type II pneumocyte number 1.87e-03 1.00e+00 abnormal pulmonary alveolus epithelium morphology 1.87e-03 1.00e+00 enlarged alveolar lamellar bodies 2.60e-03 1.00e+00 abnormal pulmonary alveolus morphology 2.72e-03 1.00e+00 increased susceptibility to viral infection 2.87e-03 1.00e+00 lung inflammation 3.74e-03 1.00e+00 abnormal respiratory mucosa morphology 3.74e-03 1.00e+00 pancreas necrosis 3.74e-03 1.00e+00 abnormal pulmonary alveolar parenchyma morphology 5.61e-03 1.00e+00 increased lung compliance 5.61e-03 1.00e+00 absent alveolar lamellar bodies 5.62e-03 1.00e+00 abnormal pulmonary elastic fiber morphology 6.46e-03 1.00e+00 abnormal lipid homeostasis 7.47e-03 1.00e+00 abnormal dendritic cell chemotaxis 7.47e-03 1.00e+00 decreased lung compliance 7.48e-03 1.00e+00 abnormal respiratory system morphology

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

²FDR corrected p-value (Benjamini-Hochberg)