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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod59

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod59 Module size 67 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 92370 ACPL2 2-phosphoxylose phosphatase 1 55057 AIM1L crystallin beta-gamma domain containing 2 115701 ALPK2 alpha kinase 2 83787 ARMC10 armadillo repeat containing 10 653308 ASAH2B N-acylsphingosine amidohydrolase 2B 653308 ASAH2C N-acylsphingosine amidohydrolase 2B 148789 B3GALNT2 beta-1,3-N-acetylgalactosaminyltransferase 2 64755 C16orf58 chromosome 16 open reading frame 58 83608 C18orf21 chromosome 18 open reading frame 21 126353 C19orf21 mitotic spindle positioning 284325 C19orf54 chromosome 19 open reading frame 54 284422 C19orf77 small integral membrane protein 24 55345 C4orf21 zinc finger GRF-type containing 1 221477 C6orf89 chromosome 6 open reading frame 89 55071 C9orf40 chromosome 9 open reading frame 40 133957 CCDC127 coiled-coil domain containing 127 343099 CCDC18 coiled-coil domain containing 18 168455 CCDC71L coiled-coil domain containing 71 like 50489 CD207 CD207 molecule 56650 CLDND1 claudin domain containing 1 57699 CPNE5 copine 5 100127905 FAM165A small integral membrane protein 11 pseudogene 1 26049 FAM169A family with sequence similarity 169 member A 27146 FAM184B family with sequence similarity 184 member B 348262 FAM195B MAPK regulated corepressor interacting protein 1 254228 FAM26E calcium homeostasis modulator family member 5 286336 FAM78A family with sequence similarity 78 member A 23105 FSTL4 follistatin like 4 84750 FUT10 fucosyltransferase 10 729438 GATSL1 cytosolic arginine sensor for mTORC1 subunit 2 55830 GLT8D1 glycosyltransferase 8 domain containing 1 56927 GPR108 G protein-coupled receptor 108 57512 GPR158 G protein-coupled receptor 158 727957 HEATR7A maestro heat like repeat family member 1 643314 KIAA0754 KIAA0754 57482 KIAA1211 KIAA1211 57710 KIAA1614 KIAA1614 200634 KRTCAP3 keratinocyte associated protein 3 143903 LAYN layilin 83742 MARVELD1 MARVEL domain containing 1 100132406 NBPF10 NBPF member 10 149013 NBPF12 NBPF member 12 200030 NBPF24 NBPF member 11 400818 NBPF9 NBPF member 9 340990 OTOG otogelin 23252 OTUD3 OTU deubiquitinase 3 347862 PDDC1 glutamine amidotransferase like class 1 domain containing 1 79142 PHF23 PHD finger protein 23 400224 PLEKHD1 pleckstrin homology and coiled-coil domain containing D1 79144 PPDPF pancreatic progenitor cell differentiation and proliferation factor 390999 PRAMEF12 PRAME family member 12 375743 PTAR1 protein prenyltransferase alpha subunit repeat containing 1 84659 RNASE7 ribonuclease A family member 7 142891 SAMD8 sterile alpha motif domain containing 8 6573 SLC19A1 solute carrier family 19 member 1 5003 SLC22A18AS solute carrier family 22 member 18 antisense 55106 SLFN12 schlafen family member 12 338596 ST8SIA6 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6 26872 STEAP1 STEAP family member 1 57465 TBC1D24 TBC1 domain family member 24 340543 TCEAL5 transcription elongation factor A like 5 79905 TMC7 transmembrane channel like 7 441027 TMEM150C transmembrane protein 150C 92691 TMEM169 transmembrane protein 169 65062 TMEM237 transmembrane protein 237 129293 TRABD2A TraB domain containing 2A 81552 VOPP1 VOPP1, WBP1/VOPP1 family member

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 4.27e-02 9.84e-05 GO integral component of organelle membrane cellular_component 2.10e-02 1.50e-04 GO mechanosensitive ion channel 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 3.65e-05 7.98e-03 integral component of organelle membrane 9.14e-04 1.84e-01 ceramide biosynthetic process 1.75e-03 2.51e-01 transferase activity, transferring glycosyl groups 1.95e-03 3.34e-01 negative regulation of dendritic spine development 2.62e-03 4.24e-01 sphingolipid biosynthetic process 3.76e-03 5.67e-01 ceramide metabolic process 3.89e-03 5.71e-01 regulation of cell projection organization 3.90e-03 5.71e-01 negative regulation of collateral sprouting 4.17e-03 5.25e-01 folic acid binding 4.42e-03 6.30e-01 regulation of developmental growth 5.30e-03 7.28e-01 carbohydrate metabolic process 5.84e-03 7.72e-01 positive regulation of deacetylase activity 5.84e-03 7.72e-01 positive regulation of histone deacetylase activity 6.48e-03 7.59e-01 carbohydrate binding 6.74e-03 7.02e-01 Golgi membrane 6.78e-03 7.89e-01 brain-derived neurotrophic factor binding 6.97e-03 8.84e-01 regulation of organelle assembly 6.99e-03 8.06e-01 folic acid transporter activity 7.08e-03 8.14e-01 channel activity 7.21e-03 8.27e-01 passive transmembrane transporter activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.23e-03 3.21e-01 CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES 4.94e-03 4.53e-01 N GLYCAN ANTENNAE ELONGATION 6.55e-03 5.71e-01 ANTIGEN PROCESSING CROSS PRESENTATION 6.86e-03 5.39e-01 CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES 8.22e-03 6.86e-01 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 1.08e-02 7.78e-01 N GLYCAN ANTENNAE ELONGATION 1.08e-02 7.78e-01 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 1.68e-02 1.00e+00 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 1.97e-02 1.00e+00 GLYCOSPHINGOLIPID METABOLISM 2.24e-02 1.00e+00 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 2.25e-02 1.00e+00 ANTIGEN PROCESSING CROSS PRESENTATION 3.55e-02 1.00e+00 METABOLISM OF VITAMINS AND COFACTORS 3.59e-02 1.00e+00 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 4.68e-02 1.00e+00 SPHINGOLIPID METABOLISM

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 abnormal otolithic membrane morphology 3.74e-03 1e+00 abnormal Langerhans cell morphology 3.74e-03 1e+00 abnormal type IV hypersensitivity reaction 3.75e-03 1e+00 abnormal crista ampullaris morphology 3.75e-03 1e+00 abnormal utricle morphology 5.60e-03 1e+00 abnormal ear physiology 5.60e-03 1e+00 absent Langerhans cell 5.60e-03 1e+00 decreased Langerhans cell number 5.61e-03 1e+00 abnormal pinna reflex 5.61e-03 1e+00 absent startle reflex 5.61e-03 1e+00 abnormal otolith morphology 5.62e-03 1e+00 abnormal vestibular saccule morphology 5.62e-03 1e+00 abnormal semicircular canal morphology 5.63e-03 1e+00 abnormal lymphopoiesis 9.32e-03 1e+00 abnormal placing response 9.34e-03 1e+00 abnormal Peyer's patch morphology 1.30e-02 1e+00 abnormal tectorial membrane morphology 1.49e-02 1e+00 abnormal cochlea morphology 1.49e-02 1e+00 decreased dendritic cell number 1.67e-02 1e+00 head tilt

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

²FDR corrected p-value (Benjamini-Hochberg)