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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod105

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod105 Module size 57 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 57188 ADAMTSL3 ADAMTS like 3 60370 AVPI1 arginine vasopressin induced 1 414157 C10orf62 chromosome 10 open reading frame 62 399947 C11orf87 chromosome 11 open reading frame 87 55337 C19orf66 chromosome 19 open reading frame 66 164127 C1orf65 coiled-coil domain containing 185 146894 CD300LG CD300 molecule like family member g 26511 CHIC2 cysteine rich hydrophobic domain 2 54544 CRCT1 cysteine rich C-terminal 1 128821 CST9L cystatin 9 like 100131997 FAM27E3 family with sequence similarity 27 member E3 401508 FAM74A2 family with sequence similarity 74 member A4 143684 FAM76B family with sequence similarity 76 member B 84892 GTDC2 protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-) 9674 KIAA0040 KIAA0040 3889 KRT83 keratin 83 386677 KRTAP10-1 keratin associated protein 10-1 386678 KRTAP10-11 keratin associated protein 10-11 386682 KRTAP10-3 keratin associated protein 10-3 386680 KRTAP10-5 keratin associated protein 10-5 386675 KRTAP10-7 keratin associated protein 10-7 386681 KRTAP10-8 keratin associated protein 10-8 386676 KRTAP10-9 keratin associated protein 10-9 353332 KRTAP12-1 keratin associated protein 12-1 353323 KRTAP12-2 keratin associated protein 12-2 337960 KRTAP13-3 keratin associated protein 13-3 388818 KRTAP26-1 keratin associated protein 26-1 653240 KRTAP4-11 keratin associated protein 4-11 83755 KRTAP4-12 keratin associated protein 4-12 85291 KRTAP4-2 keratin associated protein 4-2 100996750 KRTAP4-7 keratin-associated protein 4-7 440023 KRTAP5-6 keratin associated protein 5-6 3846 KRTAP5-9 keratin associated protein 5-9 83899 KRTAP9-2 keratin associated protein 9-2 353132 LCE1B late cornified envelope 1B 353139 LCE2A late cornified envelope 2A 353141 LCE2D late cornified envelope 2D 353144 LCE3C late cornified envelope 3C 353145 LCE3E late cornified envelope 3E 199834 LCE4A late cornified envelope 4A 4062 LY6H lymphocyte antigen 6 family member H 23005 MAPKBP1 mitogen-activated protein kinase binding protein 1 4336 MOBP myelin-associated oligodendrocyte basic protein 388677 NOTCH2NL notch 2 N-terminal like A 57532 NUFIP2 nuclear FMR1 interacting protein 2 5013 OTX1 orthodenticle homeobox 1 5620 PRM2 protamine 2 114971 PTPMT1 protein tyrosine phosphatase, mitochondrial 1 4184 SMCP sperm mitochondria associated cysteine rich protein 130560 SPATA3 spermatogenesis associated 3 221409 SPATA8 spermatogenesis associated serine rich 1 6691 SPINK2 serine peptidase inhibitor, Kazal type 2 56906 THAP10 THAP domain containing 10 152815 THAP6 THAP domain containing 6 64129 TINAGL1 tubulointerstitial nephritis antigen like 1 129303 TMEM150A transmembrane protein 150A 280664 WFDC10B WAP four-disulfide core domain 10B

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 6.05e-02 9.04e-28 GO keratin filament cellular_component 5.12e-02 5.64e-37 GO keratinization biological_process 1.36e-02 3.20e-09 GO peptide cross-linking biological_process 5.42e-03 4.83e-35 Reactome Keratinization Developmental Biology

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 epithelial cell differentiation 0.00e+00 0.00e+00 keratinocyte differentiation 0.00e+00 0.00e+00 epidermal cell differentiation 0.00e+00 0.00e+00 epidermis development 0.00e+00 0.00e+00 keratinization 0.00e+00 0.00e+00 skin development 0.00e+00 0.00e+00 keratin filament 0.00e+00 0.00e+00 intermediate filament cytoskeleton 0.00e+00 0.00e+00 supramolecular fiber 0.00e+00 0.00e+00 intermediate filament 4.63e-09 3.15e-06 peptide cross-linking 2.18e-08 8.27e-06 cornified envelope 4.30e-07 1.46e-04 structural molecule activity 3.81e-04 6.63e-02 peptidase inhibitor activity 4.10e-04 9.52e-02 hair cycle 1.95e-03 3.34e-01 brain morphogenesis 1.95e-03 3.34e-01 forebrain morphogenesis 1.95e-03 3.34e-01 diencephalon morphogenesis 2.27e-03 3.15e-01 enzyme inhibitor activity 3.90e-03 5.71e-01 cardiolipin biosynthetic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 absent Harderian gland 1.87e-03 1e+00 retina hyperplasia 1.87e-03 1e+00 delayed fertility 1.87e-03 1e+00 abnormal trigeminal V mesencephalic nucleus morphology 1.87e-03 1e+00 increased cornea thickness 1.87e-03 1e+00 decreased superior colliculus size 1.87e-03 1e+00 abnormal orbitosphenoid bone morphology 1.88e-03 1e+00 meteorism 3.74e-03 1e+00 decreased inferior colliculus size 3.74e-03 1e+00 abnormal pituitary secretion 3.74e-03 1e+00 nonconvulsive seizures 3.74e-03 1e+00 increased superior colliculus size 3.74e-03 1e+00 absent lacrimal glands 3.74e-03 1e+00 absent lateral semicircular canal 5.60e-03 1e+00 increased inferior colliculus size 5.61e-03 1e+00 decreased midbrain size 5.61e-03 1e+00 absent semicircular canals 5.61e-03 1e+00 abnormal eye anterior chamber morphology 5.62e-03 1e+00 small hippocampus 7.48e-03 1e+00 abnormal vestibular saccule morphology

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

²FDR corrected p-value (Benjamini-Hochberg)