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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod209

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod209 Module size 21 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 21 ABCA3 ATP binding cassette subfamily A member 3 159686 CCDC147 cilia and flagella associated protein 58 92558 CCDC64 BICD family like cargo adaptor 1 89832 CHRFAM7A CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion 90527 DUOXA1 dual oxidase maturation factor 1 405753 DUOXA2 dual oxidase maturation factor 2 56478 EIF4ENIF1 eukaryotic translation initiation factor 4E nuclear import factor 1 2016 EMX1 empty spiracles homeobox 1 2018 EMX2 empty spiracles homeobox 2 143879 KBTBD3 kelch repeat and BTB domain containing 3 84445 LZTS2 leucine zipper tumor suppressor 2 54842 MFSD6 major facilitator superfamily domain containing 6 162387 MFSD6L major facilitator superfamily domain containing 6 like 89797 NAV2 neuron navigator 2 89795 NAV3 neuron navigator 3 344022 NOTO notochord homeobox 57575 PCDH10 protocadherin 10 23328 SASH1 SAM and SH3 domain containing 1 55238 SLC38A7 solute carrier family 38 member 7 164656 TMPRSS6 transmembrane serine protease 6 55100 WDR70 WD repeat domain 70

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).

No specific annotations were found for this module

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 5.64e-06 2.31e-03 regulation of thyroid hormone generation 2.25e-05 7.97e-03 cerebral cortex regionalization 3.99e-05 1.32e-02 telencephalon regionalization 4.23e-05 1.39e-02 regulation of hormone metabolic process 6.05e-05 1.89e-02 forebrain regionalization 1.69e-04 4.55e-02 hydrogen peroxide metabolic process 1.45e-03 2.67e-01 response to drug 1.51e-03 2.07e-01 alveolar lamellar body 1.53e-03 2.79e-01 reactive oxygen species metabolic process 1.85e-03 3.25e-01 cerebral cortex development 1.95e-03 3.34e-01 vagus nerve development 1.97e-03 2.78e-01 L-aspartate transmembrane transporter activity 2.78e-03 4.45e-01 pattern specification process 3.89e-03 5.71e-01 glutamine transport 3.89e-03 5.71e-01 radial glial cell differentiation 3.89e-03 5.71e-01 regulation of systemic arterial blood pressure by baroreceptor feedback 3.89e-03 5.71e-01 regulation of protein autoubiquitination 3.90e-03 5.71e-01 neurological system process involved in regulation of systemic arterial blood pressure 3.94e-03 5.00e-01 L-glutamine transmembrane transporter activity 3.94e-03 5.00e-01 L-serine transmembrane transporter activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.29e-03 3.25e-01 ACETYLCHOLINE BINDING AND DOWNSTREAM EVENTS 3.29e-03 3.25e-01 HIGHLY CALCIUM PERMEABLE POSTSYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 9.97e-03 7.99e-01 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 1.00e-02 7.99e-01 TRANSMISSION ACROSS CHEMICAL SYNAPSES 1.28e-02 8.97e-01 ABCA TRANSPORTERS IN LIPID HOMEOSTASIS 1.56e-02 1.00e+00 ABC FAMILY PROTEINS MEDIATED TRANSPORT 1.68e-02 1.00e+00 NEURONAL SYSTEM 1.95e-02 1.00e+00 ABCA TRANSPORTERS IN LIPID HOMEOSTASIS 2.14e-02 1.00e+00 HIGHLY CALCIUM PERMEABLE POSTSYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 2.67e-02 1.00e+00 ACETYLCHOLINE BINDING AND DOWNSTREAM EVENTS 2.91e-02 1.00e+00 ABC FAMILY PROTEINS MEDIATED TRANSPORT 4.66e-02 1.00e+00 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.74e-03 1e+00 dilated seminal vesicles 3.75e-03 1e+00 abnormal hippocampal fornix morphology 3.75e-03 1e+00 abnormal hair follicle infundibulum morphology 5.61e-03 1e+00 increased wet-to-dry lung weight ratio 5.62e-03 1e+00 abnormal heart iron level 5.62e-03 1e+00 abnormal ovary development 5.63e-03 1e+00 gonadal ridge hypoplasia 5.64e-03 1e+00 absent oviduct 5.64e-03 1e+00 absent efferent ductules of testis 5.64e-03 1e+00 abnormal pallium development 7.49e-03 1e+00 decreased anterior commissure size 7.49e-03 1e+00 abnormal ureteric bud tip morphology 7.50e-03 1e+00 absent uterus 7.51e-03 1e+00 abnormal metanephric ureteric bud development 9.32e-03 1e+00 abnormal intestinal mineral absorption 9.33e-03 1e+00 abnormal embryonic cilium location or orientation 9.33e-03 1e+00 decreased vertebrae number 9.35e-03 1e+00 double ureter 9.35e-03 1e+00 abnormal uterine horn morphology 9.35e-03 1e+00 truncated notochord

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

²FDR corrected p-value (Benjamini-Hochberg)