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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod172

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod172 Module size 46 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 58527 ABRACL ABRA C-terminal like 161502 C15orf26 cilia and flagella associated protein 161 375307 C2orf62 ciliogenesis associated TTC17 interacting protein 154313 C6orf165 cilia and flagella associated protein 206 29070 CCDC113 coiled-coil domain containing 113 85478 CCDC65 coiled-coil domain containing 65 257236 CCDC96 coiled-coil domain containing 96 123872 DNAAF1 dynein axonemal assembly factor 1 114327 EFHC1 EF-hand domain containing 1 219670 ENKUR enkurin, TRPC channel interacting protein 730112 FAM166B family with sequence similarity 166 member B 123811 FOPNL FGFR1OP N-terminal like 3359 HTR3A 5-hydroxytryptamine receptor 3A 9177 HTR3B 5-hydroxytryptamine receptor 3B 170572 HTR3C 5-hydroxytryptamine receptor 3C 200909 HTR3D 5-hydroxytryptamine receptor 3D 285242 HTR3E 5-hydroxytryptamine receptor 3E 54768 HYDIN HYDIN, axonemal central pair apparatus protein 115811 IQCD IQ motif containing D 389434 IYD iodotyrosine deiodinase 167691 LCA5 LCA5, lebercilin 987 LRBA LPS responsive beige-like anchor protein 151827 LRRC34 leucine rich repeat containing 34 11165 NUDT3 nudix hydrolase 3 113746 ODF3 outer dense fiber of sperm tails 3 133015 PACRGL parkin coregulated like 139212 PIH1D3 PIH1 domain containing 3 57333 RCN3 reticulocalbin 3 158787 RIBC1 RIB43A domain with coiled-coils 1 345895 RSPH4A radial spoke head component 4A 81492 RSPH6A radial spoke head 6 homolog A 221421 RSPH9 radial spoke head 9 homolog 154075 SAMD3 sterile alpha motif domain containing 3 11063 SOX30 SRY-box 30 128153 SPATA17 spermatogenesis associated 17 55296 TBC1D19 TBC1 domain family member 19 200132 TCTEX1D1 Tctex1 domain containing 1 255758 TCTEX1D2 Tctex1 domain containing 2 27285 TEKT2 tektin 2 64518 TEKT3 tektin 3 150483 TEKT4 tektin 4 146279 TEKT5 tektin 5 56255 TMX4 thioredoxin related transmembrane protein 4 9654 TTLL4 tubulin tyrosine ligase like 4 149465 WDR65 cilia and flagella associated protein 57 201181 ZNF385C zinc finger protein 385C

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 3.00e-01 2.39e-12 GO cilium movement involved in cell motility biological_process 2.70e-01 4.38e-12 GO serotonin receptor signaling pathway biological_process 8.56e-02 7.08e-07 GO axonemal dynein complex assembly biological_process 4.50e-02 1.10e-09 GO cilium movement 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 organelle assembly 0.00e+00 0.00e+00 cilium assembly 0.00e+00 0.00e+00 cell projection assembly 0.00e+00 0.00e+00 cilium organization 0.00e+00 0.00e+00 cilium movement 0.00e+00 0.00e+00 motile cilium 0.00e+00 0.00e+00 cilium 5.27e-13 3.65e-10 serotonin-gated cation-selective channel activity 1.40e-11 1.25e-08 cilium movement involved in cell motility 7.88e-11 6.60e-08 axoneme assembly 7.54e-10 5.70e-07 microtubule-based process 7.99e-10 6.02e-07 microtubule-based movement 1.40e-09 1.02e-06 microtubule bundle formation 1.68e-09 1.21e-06 cilium-dependent cell motility 1.74e-09 1.25e-06 cilium or flagellum-dependent cell motility 4.22e-09 2.04e-06 transmitter-gated ion channel activity 4.68e-09 1.93e-06 sperm flagellum 9.44e-09 3.76e-06 axoneme 1.44e-08 9.19e-06 flagellated sperm motility 1.84e-08 1.16e-05 sperm motility

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 4.85e-08 1.30e-05 LIGAND GATED ION CHANNEL TRANSPORT 9.29e-07 1.62e-04 LIGAND GATED ION CHANNEL TRANSPORT 1.52e-05 2.82e-03 ION CHANNEL TRANSPORT 9.11e-05 1.17e-02 ION CHANNEL TRANSPORT 1.12e-03 1.30e-01 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 9.61e-03 7.76e-01 AMINE DERIVED HORMONES 4.34e-02 1.00e+00 AMINE DERIVED HORMONES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 9.34e-06 4.51e-02 abnormal mucociliary clearance 1.12e-05 5.09e-02 abnormal brain ependyma motile cilium physiology 5.13e-05 1.45e-01 abnormal respiratory motile cilium morphology 6.78e-05 1.75e-01 abnormal respiratory motile cilium physiology 3.21e-04 4.69e-01 hairpin sperm flagellum 5.40e-04 6.37e-01 enlarged brain ventricles 6.06e-04 6.78e-01 asthenozoospermia 1.46e-03 1.00e+00 cachexia 1.87e-03 1.00e+00 rhinitis 1.87e-03 1.00e+00 urinary bladder obstruction 1.87e-03 1.00e+00 abnormal urinary bladder detrusor smooth muscle morphology 1.87e-03 1.00e+00 increased urinary bladder weight 3.74e-03 1.00e+00 abnormal ependyma motile cilium morphology 3.74e-03 1.00e+00 enlarged parietal bone 3.74e-03 1.00e+00 abnormal brain meninges morphology 3.74e-03 1.00e+00 prostate gland inflammation 3.74e-03 1.00e+00 abnormal urinary bladder urothelium morphology 3.74e-03 1.00e+00 neurogenic bladder 3.74e-03 1.00e+00 pyelonephritis 5.61e-03 1.00e+00 abnormal aggression-related behavior

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

²FDR corrected p-value (Benjamini-Hochberg)