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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod12

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod12 Module size 40 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 11149 BVES blood vessel epicardial substance 55765 C1orf106 innate immunity activator 90060 CCDC120 coiled-coil domain containing 120 285025 CCDC141 coiled-coil domain containing 141 27185 DISC1 DISC1 scaffold protein 165215 FAM171B family with sequence similarity 171 member B 55691 FRMD4A FERM domain containing 4A 23150 FRMD4B FERM domain containing 4B 392465 GLOD5 glyoxalase domain containing 5 84868 HAVCR2 hepatitis A virus cellular receptor 2 55846 ITFG2 integrin alpha FG-GAP repeat containing 2 10962 MLLT11 MLLT11, transcription factor 7 cofactor 758 MPPED1 metallophosphoesterase domain containing 1 4753 NELL2 neural EGFL like 2 22829 NLGN4Y neuroligin 4 Y-linked 9378 NRXN1 neurexin 1 9379 NRXN2 neurexin 2 30010 NXPH1 neurexophilin 1 11249 NXPH2 neurexophilin 2 11142 PKIG cAMP-dependent protein kinase inhibitor gamma 64091 POPDC2 popeye domain containing 2 64208 POPDC3 popeye domain containing 3 79608 RIC3 RIC3 acetylcholine receptor chaperone 79641 ROGDI rogdi homolog 22902 RUFY3 RUN and FYVE domain containing 3 55974 SLC50A1 solute carrier family 50 member 1 6853 SYN1 synapsin I 8224 SYN3 synapsin III 341359 SYT10 synaptotagmin 10 57586 SYT13 synaptotagmin 13 255928 SYT14 synaptotagmin 14 83851 SYT16 synaptotagmin 16 148281 SYT6 synaptotagmin 6 143425 SYT9 synaptotagmin 9 83604 TMEM47 transmembrane protein 47 25789 TMEM59L transmembrane protein 59 like 162461 TMEM92 transmembrane protein 92 7442 TRPV1 transient receptor potential cation channel subfamily V member 1 51393 TRPV2 transient receptor potential cation channel subfamily V member 2 7102 TSPAN7 tetraspanin 7

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 1.30e-01 5.90e-07 GO postsynaptic membrane assembly biological_process 3.18e-02 1.85e-07 GO synaptic vesicle exocytosis biological_process 3.11e-02 1.85e-07 GO exocytic vesicle cellular_component 2.26e-02 2.54e-06 GO vocalization behavior biological_process 1.84e-02 1.22e-05 GO cAMP binding molecular_function 1.52e-02 5.03e-07 GO neurotransmitter secretion biological_process 6.95e-03 2.93e-04 GO establishment of epithelial cell polarity biological_process 5.71e-03 4.42e-07 GO regulation of dopamine secretion biological_process

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 neurotransmitter transport 0.00e+00 0.00e+00 regulation of neurotransmitter levels 0.00e+00 0.00e+00 neurotransmitter secretion 2.24e-11 1.98e-08 chemical synaptic transmission 6.73e-10 5.11e-07 calcium ion-regulated exocytosis of neurotransmitter 7.65e-10 5.78e-07 regulation of calcium ion-dependent exocytosis 7.68e-10 4.15e-07 calcium-dependent phospholipid binding 1.11e-09 5.85e-07 clathrin binding 5.33e-09 2.53e-06 syntaxin binding 2.52e-08 1.56e-05 regulation of regulated secretory pathway 2.90e-08 1.77e-05 synaptic vesicle exocytosis 3.71e-08 1.53e-05 SNARE binding 6.81e-08 3.95e-05 calcium ion regulated exocytosis 7.02e-08 4.07e-05 vesicle fusion 2.96e-07 1.55e-04 synaptic vesicle transport 3.36e-07 1.74e-04 regulation of exocytosis 4.81e-07 2.42e-04 organelle fusion 5.14e-07 1.57e-04 presynapse 1.11e-06 5.23e-04 membrane fusion 1.34e-06 6.22e-04 vesicle localization

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 8.79e-06 1.70e-03 DOPAMINE NEUROTRANSMITTER RELEASE CYCLE 9.34e-06 1.40e-03 DOPAMINE NEUROTRANSMITTER RELEASE CYCLE 5.92e-05 9.72e-03 NEUROTRANSMITTER RELEASE CYCLE 6.29e-05 1.03e-02 TRANSMISSION ACROSS CHEMICAL SYNAPSES 2.01e-04 2.38e-02 NEUROTRANSMITTER RELEASE CYCLE 7.59e-04 7.85e-02 TRANSMISSION ACROSS CHEMICAL SYNAPSES 1.19e-03 1.17e-01 NEURONAL SYSTEM 5.00e-03 4.57e-01 NEURONAL SYSTEM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.98e-06 2.93e-02 abnormal social investigation 9.10e-06 4.43e-02 altered response of heart to induced stress 6.42e-05 1.68e-01 abnormal sinoatrial node morphology 1.73e-04 3.21e-01 sinus bradycardia 2.41e-04 3.93e-01 abnormal inhibitory postsynaptic currents 3.25e-04 4.72e-01 impaired social transmission of food preference 4.82e-04 5.95e-01 increased synaptic depression 4.88e-04 5.99e-01 abnormal sinoatrial node conduction 2.49e-03 1.00e+00 abnormal response to novel object 3.76e-03 1.00e+00 abnormal latent inhibition of conditioning behavior 5.62e-03 1.00e+00 increased coronary flow rate 6.85e-03 1.00e+00 decreased prepulse inhibition 7.48e-03 1.00e+00 abnormal urination 7.49e-03 1.00e+00 increased left ventricle developed pressure 7.49e-03 1.00e+00 abnormal CNS synapse formation 9.33e-03 1.00e+00 delayed axon extension 9.34e-03 1.00e+00 decreased T follicular helper cell number 9.34e-03 1.00e+00 abnormal sensory neuron physiology 9.34e-03 1.00e+00 abnormal impulsive behavior control 9.36e-03 1.00e+00 increased blood osmolality

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

²FDR corrected p-value (Benjamini-Hochberg)