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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod193

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod193 Module size 31 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1636 ACE angiotensin I converting enzyme 59272 ACE2 angiotensin I converting enzyme 2 632 BGLAP bone gamma-carboxyglutamate protein 671 BPI bactericidal permeability increasing protein 389941 C1QL3 complement C1q like 3 1473 CST5 cystatin D 8530 CST7 cystatin F 1475 CSTA cystatin A 1476 CSTB cystatin B 1508 CTSB cathepsin B 1075 CTSC cathepsin C 1512 CTSH cathepsin H 1513 CTSK cathepsin K 1514 CTSL1 cathepsin L 1515 CTSL2 cathepsin V 1513 CTSO cathepsin K 1520 CTSS cathepsin S 1522 CTSZ cathepsin Z 2896 GRN granulin precursor 9452 ITM2A integral membrane protein 2A 81618 ITM2C integral membrane protein 2C 56660 KCNK12 potassium two pore domain channel subfamily K member 12 390940 PINLYP phospholipase A2 inhibitor and LY6/PLAUR domain containing 5972 REN renin 347735 SERINC2 serine incorporator 2 871 SERPINH1 serpin family H member 1 142680 SLC34A3 solute carrier family 34 member 3 6590 SLPI secretory leukocyte peptidase inhibitor 6692 SPINT1 serine peptidase inhibitor, Kunitz type 1 6768 ST14 suppression of tumorigenicity 14 81622 UNC93B1 unc-93 homolog B1, TLR signaling regulator

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 1.57e-01 2.14e-09 GO angiotensin maturation biological_process 1.46e-01 1.65e-05 GO peptidyl-dipeptidase activity molecular_function 1.02e-01 4.64e-09 Reactome Trafficking and processing of endosomal TLR Immune System 5.22e-02 3.86e-13 GO proteolysis involved in cellular protein catabolic process biological_process 4.05e-02 7.08e-07 GO proteoglycan binding molecular_function 2.84e-02 5.06e-03 Reactome Type II Na+/Pi cotransporters Transport of small molecules 2.81e-02 1.22e-06 GO cellular response to thyroid hormone stimulus biological_process 2.26e-02 1.57e-09 GO cysteine-type peptidase activity molecular_function 1.87e-02 7.49e-06 GO cysteine-type endopeptidase inhibitor activity 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 9.82e-10 5.23e-07 endopeptidase activity 1.15e-09 6.04e-07 cysteine-type endopeptidase activity 3.12e-09 2.18e-06 protein maturation 8.37e-09 3.36e-06 lysosome 1.10e-08 7.12e-06 multicellular organismal macromolecule metabolic process 2.79e-08 1.71e-05 protein processing 3.34e-08 1.23e-05 vacuole 4.25e-08 2.54e-05 multicellular organism metabolic process 6.73e-08 2.65e-05 peptidase activity 6.76e-08 2.38e-05 endolysosome lumen 9.88e-08 5.59e-05 angiotensin maturation 1.22e-07 6.80e-05 regulation of angiotensin metabolic process 1.43e-07 5.37e-05 serine-type peptidase activity 1.54e-07 5.75e-05 serine hydrolase activity 2.06e-07 1.10e-04 regulation of systemic arterial blood pressure by circulatory renin-angiotensin 2.13e-07 1.14e-04 neutrophil mediated immunity 3.43e-07 1.19e-04 endopeptidase inhibitor activity 4.07e-07 1.39e-04 peptidase inhibitor activity 5.02e-07 2.53e-04 regulation of systemic arterial blood pressure by renin-angiotensin 5.53e-07 2.76e-04 regulation of blood volume by renin-angiotensin

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 MHC CLASS II ANTIGEN PRESENTATION 1.12e-11 3.27e-09 TRAFFICKING AND PROCESSING OF ENDOSOMAL TLR 4.78e-11 1.78e-08 MHC CLASS II ANTIGEN PRESENTATION 2.58e-10 9.01e-08 TRAFFICKING AND PROCESSING OF ENDOSOMAL TLR 1.48e-08 3.19e-06 TOLL RECEPTOR CASCADES 3.22e-08 8.86e-06 TOLL RECEPTOR CASCADES 9.81e-06 1.46e-03 INNATE IMMUNE SYSTEM 2.11e-05 3.79e-03 INNATE IMMUNE SYSTEM 6.86e-03 5.92e-01 ENDOSOMAL VACUOLAR PATHWAY 1.38e-02 9.51e-01 ENDOSOMAL VACUOLAR PATHWAY 1.99e-02 1.00e+00 LYSOSOME VESICLE BIOGENESIS 4.21e-02 1.00e+00 ANTIGEN PROCESSING CROSS PRESENTATION 4.29e-02 1.00e+00 LYSOSOME VESICLE BIOGENESIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.68e-04 3.15e-01 hypotension 4.70e-04 5.86e-01 kidney medulla atrophy 5.34e-04 6.32e-01 amyloidosis 6.29e-04 6.91e-01 kidney papillary atrophy 8.67e-04 8.32e-01 kidney cortex atrophy 1.35e-03 1.00e+00 abnormal kidney medulla morphology 1.67e-03 1.00e+00 increased circulating creatinine level 2.42e-03 1.00e+00 insulitis 2.65e-03 1.00e+00 kidney atrophy 3.19e-03 1.00e+00 renal tubule atrophy 3.74e-03 1.00e+00 impaired stratum corneum desquamation 4.55e-03 1.00e+00 abnormal kidney cortex morphology 4.85e-03 1.00e+00 salivary gland inflammation 5.64e-03 1.00e+00 abnormal juxtaglomerular cell morphology 5.64e-03 1.00e+00 increased interferon-alpha secretion 6.29e-03 1.00e+00 decreased susceptibility to autoimmune diabetes 6.71e-03 1.00e+00 decreased systemic arterial systolic blood pressure 7.51e-03 1.00e+00 decreased susceptibility to induced pancreatitis 8.15e-03 1.00e+00 decreased circulating interleukin-6 level 9.36e-03 1.00e+00 abnormal stratum corneum lipid matrix formation

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

²FDR corrected p-value (Benjamini-Hochberg)