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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod44

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod44 Module size 61 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 64400 AKTIP AKT interacting protein 259173 ALS2CL ALS2 C-terminal like 11151 CORO1A coronin 1A 57175 CORO1B coronin 1B 23603 CORO1C coronin 1C 7464 CORO2A coronin 2A 10391 CORO2B coronin 2B 84940 CORO6 coronin 6 27123 DKK2 dickkopf WNT signaling pathway inhibitor 2 54455 FBXO42 F-box protein 42 56704 JPH1 junctophilin 1 57158 JPH2 junctophilin 2 57338 JPH3 junctophilin 3 84502 JPH4 junctophilin 4 122773 KLHDC1 kelch domain containing 1 23008 KLHDC10 kelch domain containing 10 23588 KLHDC2 kelch domain containing 2 116138 KLHDC3 kelch domain containing 3 126823 KLHDC9 kelch domain containing 9 3848 KRT1 keratin 1 3852 KRT5 keratin 5 3853 KRT6A keratin 6A 3854 KRT6B keratin 6B 286887 KRT6C keratin 6C 3855 KRT7 keratin 7 9119 KRT75 keratin 75 3888 KRT82 keratin 82 3890 KRT84 keratin 84 315218 LMF1 lipase maturation factor 2 84466 MEGF10 multiple EGF like domains 10 84465 MEGF11 multiple EGF like domains 11 1953 MEGF6 multiple EGF like domains 6 79906 MORN1 MORN repeat containing 1 283385 MORN3 MORN repeat containing 3 118812 MORN4 MORN repeat containing 4 51168 MYO15A myosin XVA 53904 MYO3A myosin IIIA 140469 MYO3B myosin IIIB 4645 MYO5B myosin VB 55930 MYO5C myosin VC 4647 MYO7A myosin VIIA 4648 MYO7B myosin VIIB 375033 PEAR1 platelet endothelial aggregation receptor 1 57047 PLSCR2 phospholipid scramblase 2 57048 PLSCR3 phospholipid scramblase 3 389158 PLSCR5 phospholipid scramblase family member 5 10244 RABEPK Rab9 effector protein with kelch motifs 10137 RBM12 RNA binding motif protein 12 389677 RBM12B RNA binding motif protein 12B 89765 RSPH1 radial spoke head component 1 222967 RSPH10B radial spoke head 10 homolog B 728194 RSPH10B2 radial spoke head 10 homolog B2 8578 SCARF1 scavenger receptor class F member 1 91179 SCARF2 scavenger receptor class F member 2 124976 SPNS2 sphingolipid transporter 2 201305 SPNS3 sphingolipid transporter 3 (putative) 7130 TNFAIP6 TNF alpha induced protein 6 158135 TTLL11 tubulin tyrosine ligase like 11 440307 TTLL13 tubulin tyrosine ligase like 13, pseudogene 284076 TTLL6 tubulin tyrosine ligase like 6 79739 TTLL7 tubulin tyrosine ligase like 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 2.92e-01 1.87e-09 GO junctional membrane complex cellular_component 1.73e-01 1.14e-06 GO phospholipid scrambling biological_process 9.64e-02 3.33e-06 GO protein polyglutamylation biological_process 8.45e-02 2.96e-10 GO myosin complex cellular_component 6.55e-02 2.61e-08 GO calcium ion transport into cytosol biological_process 5.51e-02 1.59e-04 GO microtubule severing biological_process 3.55e-02 1.36e-05 GO stereocilium tip cellular_component 2.97e-02 1.12e-05 GO structural constituent of epidermis molecular_function 2.70e-02 7.40e-12 GO keratin filament cellular_component 2.40e-02 9.53e-08 GO regulation of ryanodine-sensitive calcium-release channel activity biological_process 1.76e-02 2.09e-11 GO cornification biological_process 1.51e-02 3.49e-05 GO phagocytic cup cellular_component 1.06e-02 3.77e-08 GO calcium-release channel activity molecular_function 3.37e-03 3.33e-06 GO phospholipid scramblase 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 7.60e-12 6.87e-09 cornification 4.05e-11 2.55e-08 actin binding 8.31e-10 6.25e-07 keratinization 8.64e-10 6.48e-07 epidermal cell differentiation 2.10e-09 9.09e-07 supramolecular fiber 3.62e-09 1.52e-06 actin cytoskeleton 5.03e-09 3.40e-06 keratinocyte differentiation 6.11e-09 2.49e-06 myosin complex 7.11e-09 2.88e-06 junctional membrane complex 8.57e-09 3.43e-06 keratin filament 2.02e-08 1.26e-05 epidermis development 2.41e-08 9.10e-06 junctional sarcoplasmic reticulum membrane 5.02e-08 2.02e-05 actin filament binding 5.29e-08 2.11e-05 motor activity 8.08e-08 4.63e-05 skin development 2.22e-07 7.11e-05 intermediate filament 2.46e-07 1.30e-04 regulation of ryanodine-sensitive calcium-release channel activity 3.65e-07 1.88e-04 regulation of release of sequestered calcium ion into cytosol 7.49e-07 2.24e-04 intermediate filament cytoskeleton 1.04e-06 3.28e-04 phospholipid scramblase 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 REGULATION OF WATER BALANCE BY RENAL AQUAPORINS 6.14e-03 4.88e-01 REGULATION OF WATER BALANCE BY RENAL AQUAPORINS 1.26e-02 8.86e-01 AQUAPORIN MEDIATED TRANSPORT 1.92e-02 1.00e+00 AQUAPORIN MEDIATED TRANSPORT 1.99e-02 1.00e+00 ACTIVATION OF CHAPERONE GENES BY XBP1S 2.34e-02 1.00e+00 UNFOLDED PROTEIN RESPONSE 4.70e-02 1.00e+00 DIABETES PATHWAYS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.65e-04 4.15e-01 abnormal horizontal cell morphology 2.67e-04 4.17e-01 abnormal auditory brainstem response 3.55e-04 4.95e-01 absent pinna reflex 8.86e-04 8.39e-01 abnormal eye size 9.65e-04 8.87e-01 increased susceptibility to systemic lupus erythematosus 1.60e-03 1.00e+00 head shaking 2.14e-03 1.00e+00 abnormal pupil morphology 2.24e-03 1.00e+00 decreased cochlear outer hair cell number 3.14e-03 1.00e+00 abnormal cochlear outer hair cell morphology 3.60e-03 1.00e+00 head tilt 3.73e-03 1.00e+00 narrow eye opening 5.03e-03 1.00e+00 abnormal cochlear hair cell morphology 5.16e-03 1.00e+00 increased circulating triglyceride level 5.40e-03 1.00e+00 head bobbing 5.67e-03 1.00e+00 impaired macrophage phagocytosis 6.82e-03 1.00e+00 decreased monocyte cell number 7.50e-03 1.00e+00 decreased lipoprotein lipase activity 7.73e-03 1.00e+00 abnormal organ of Corti morphology 8.59e-03 1.00e+00 decreased T cell number 9.36e-03 1.00e+00 decreased triglyceride lipase activity

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

²FDR corrected p-value (Benjamini-Hochberg)