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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod215

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod215 Module size 21 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 165 AEBP1 AE binding protein 1 56265 CPXM1 carboxypeptidase X, M14 family member 1 119587 CPXM2 carboxypeptidase X, M14 family member 2 8532 CPZ carboxypeptidase Z 5045 FURIN furin, paired basic amino acid cleaving enzyme 5122 PCSK1 proprotein convertase subtilisin/kexin type 1 27344 PCSK1N proprotein convertase subtilisin/kexin type 1 inhibitor 5126 PCSK2 proprotein convertase subtilisin/kexin type 2 54760 PCSK4 proprotein convertase subtilisin/kexin type 4 5125 PCSK5 proprotein convertase subtilisin/kexin type 5 5046 PCSK6 proprotein convertase subtilisin/kexin type 6 9159 PCSK7 proprotein convertase subtilisin/kexin type 7 5545 PRB4 proline rich protein BstNI subfamily 4 284654 RSPO1 R-spondin 1 84870 RSPO3 R-spondin 3 343637 RSPO4 R-spondin 4 6447 SCG5 secretogranin V 23230 VPS13A vacuolar protein sorting 13 homolog A 157680 VPS13B vacuolar protein sorting 13 homolog B 54832 VPS13C vacuolar protein sorting 13 homolog C 55187 VPS13D vacuolar protein sorting 13 homolog D

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 2.38e-01 1.75e-20 GO peptide hormone processing biological_process 1.31e-01 4.59e-09 Reactome Expression and Processing of Neurotrophins Signal Transduction 1.30e-01 4.59e-09 Reactome NGF processing Signal Transduction 1.08e-01 1.06e-09 GO peptide metabolic process biological_process 4.38e-02 6.33e-19 GO protein processing biological_process 2.55e-02 1.51e-06 Reactome Regulation of FZD by ubiquitination Signal Transduction 5.18e-04 2.15e-08 GO metallocarboxypeptidase 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 0.00e+00 0.00e+00 cellular amide metabolic process 0.00e+00 0.00e+00 peptide metabolic process 0.00e+00 0.00e+00 protein processing 0.00e+00 0.00e+00 protein maturation 0.00e+00 0.00e+00 peptide hormone processing 0.00e+00 0.00e+00 hormone metabolic process 5.61e-10 3.10e-07 peptidase activity 3.12e-09 2.18e-06 regulation of hormone levels 3.48e-08 1.44e-05 serine-type endopeptidase activity 4.84e-08 2.87e-05 nerve growth factor processing 5.89e-08 2.34e-05 serine-type peptidase activity 6.79e-08 2.67e-05 serine hydrolase activity 8.77e-07 2.82e-04 metallocarboxypeptidase activity 1.01e-06 2.95e-04 secretory granule 2.26e-06 6.72e-04 carboxypeptidase activity 3.65e-06 1.04e-03 endopeptidase activity 6.82e-06 1.84e-03 metalloexopeptidase activity 9.42e-06 3.67e-03 positive regulation of Wnt signaling pathway 2.62e-05 6.31e-03 nerve growth factor binding 2.94e-05 7.02e-03 heparin binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 7.97e-05 1.27e-02 SIGNALLING BY NGF 9.23e-05 1.44e-02 SIGNALING BY NODAL 2.69e-04 3.72e-02 INSULIN SYNTHESIS AND PROCESSING 3.31e-04 3.75e-02 SIGNALING BY NODAL 3.66e-04 4.10e-02 INSULIN SYNTHESIS AND PROCESSING 2.07e-03 1.92e-01 SIGNALLING BY NGF 5.42e-03 4.39e-01 GAMMA CARBOXYLATION TRANSPORT AND AMINO TERMINAL CLEAVAGE OF PROTEINS 6.96e-03 5.45e-01 DIABETES PATHWAYS 7.22e-03 5.62e-01 PEPTIDE HORMONE BIOSYNTHESIS 7.76e-03 6.55e-01 DIABETES PATHWAYS 1.30e-02 9.80e-01 PEPTIDE HORMONE BIOSYNTHESIS 1.34e-02 1.00e+00 GAMMA CARBOXYLATION TRANSPORT AND AMINO TERMINAL CLEAVAGE OF PROTEINS 1.46e-02 9.94e-01 PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION 1.49e-02 1.00e+00 SYNTHESIS SECRETION AND INACTIVATION OF GIP 1.53e-02 1.00e+00 TGF BETA RECEPTOR SIGNALING ACTIVATES SMADS 1.62e-02 1.00e+00 SYNTHESIS SECRETION AND INACTIVATION OF GIP 1.80e-02 1.00e+00 PRE NOTCH PROCESSING IN GOLGI 1.83e-02 1.00e+00 SYNTHESIS SECRETION AND INACTIVATION OF GLP1 1.94e-02 1.00e+00 INCRETIN SYNTHESIS SECRETION AND INACTIVATION 2.22e-02 1.00e+00 PRE NOTCH PROCESSING IN GOLGI

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.69e-04 7.19e-01 transmission ratio distortion 1.00e-03 9.02e-01 decreased circulating glucagon level 2.42e-03 1.00e+00 dextrocardia 4.37e-03 1.00e+00 persistent truncus arteriosis 4.85e-03 1.00e+00 abnormal pancreatic islet morphology 5.61e-03 1.00e+00 absent midgut 5.61e-03 1.00e+00 reduced hyperactivated sperm motility 7.48e-03 1.00e+00 increased pancreatic delta cell number 7.48e-03 1.00e+00 truncated foregut 8.87e-03 1.00e+00 polyphagia 9.34e-03 1.00e+00 decreased follicular dendritic cell number 9.36e-03 1.00e+00 chronic diarrhea 1.12e-02 1.00e+00 analgesia 1.12e-02 1.00e+00 absent sacral vertebrae 1.12e-02 1.00e+00 absent patella 1.12e-02 1.00e+00 absent anus 1.12e-02 1.00e+00 abnormal ovary development 1.21e-02 1.00e+00 reduced female fertility 1.30e-02 1.00e+00 decreased primordial ovarian follicle number 1.31e-02 1.00e+00 absent caudal vertebrae

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

²FDR corrected p-value (Benjamini-Hochberg)