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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod135

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod135 Module size 49 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 54812 AFTPH aftiphilin 55435 AP1AR adaptor related protein complex 1 associated regulatory protein 162 AP1B1 adaptor related protein complex 1 subunit beta 1 164 AP1G1 adaptor related protein complex 1 subunit gamma 1 8906 AP1G2 adaptor related protein complex 1 subunit gamma 2 8907 AP1M1 adaptor related protein complex 1 subunit mu 1 10053 AP1M2 adaptor related protein complex 1 subunit mu 2 1174 AP1S1 adaptor related protein complex 1 subunit sigma 1 8905 AP1S2 adaptor related protein complex 1 subunit sigma 2 130340 AP1S3 adaptor related protein complex 1 subunit sigma 3 160 AP2A1 adaptor related protein complex 2 subunit alpha 1 163 AP2B1 adaptor related protein complex 2 subunit beta 1 1173 AP2M1 adaptor related protein complex 2 subunit mu 1 1175 AP2S1 adaptor related protein complex 2 subunit sigma 1 8546 AP3B1 adaptor related protein complex 3 subunit beta 1 8120 AP3B2 adaptor related protein complex 3 subunit beta 2 26985 AP3M1 adaptor related protein complex 3 subunit mu 1 10947 AP3M2 adaptor related protein complex 3 subunit mu 2 1176 AP3S1 adaptor related protein complex 3 subunit sigma 1 10239 AP3S2 adaptor related protein complex 3 subunit sigma 2 10717 AP4B1 adaptor related protein complex 4 subunit beta 1 23431 AP4E1 adaptor related protein complex 4 subunit epsilon 1 9179 AP4M1 adaptor related protein complex 4 subunit mu 1 11154 AP4S1 adaptor related protein complex 4 subunit sigma 1 91056 AP5B1 adaptor related protein complex 5 subunit beta 1 55745 AP5M1 adaptor related protein complex 5 subunit mu 1 55317 AP5S1 adaptor related protein complex 5 subunit sigma 1 9907 AP5Z1 adaptor related protein complex 5 subunit zeta 1 55297 CCDC91 coiled-coil domain containing 91 9685 CLINT1 clathrin interactor 1 1211 CLTA clathrin light chain A 1212 CLTB clathrin light chain B 26088 GGA1 golgi associated, gamma adaptin ear containing, ARF binding protein 1 23062 GGA2 golgi associated, gamma adaptin ear containing, ARF binding protein 2 23163 GGA3 golgi associated, gamma adaptin ear containing, ARF binding protein 3 25938 HEATR5A HEAT repeat containing 5A 54497 HEATR5B HEAT repeat containing 5B 3482 IGF2R insulin like growth factor 2 receptor 83988 NCALD neurocalcin delta 25977 NECAP1 NECAP endocytosis associated 1 55707 NECAP2 NECAP endocytosis associated 2 53354 PANK1 pantothenate kinase 1 132320 SCLT1 sodium channel and clathrin linker 1 84251 SGIP1 SH3 domain GRB2 like endophilin interacting protein 1 9892 SNAP91 synaptosome associated protein 91 11037 STON1 stonin 1 85439 STON2 stonin 2 11276 SYNRG synergin gamma 10618 TGOLN2 trans-golgi network protein 2

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 6.40e-01 3.04e-29 GO clathrin adaptor complex cellular_component 1.26e-01 1.21e-08 GO AP-3 adaptor complex cellular_component 1.20e-01 2.10e-23 Reactome Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters Disease 1.08e-01 7.41e-14 GO clathrin coat assembly biological_process 6.78e-02 1.93e-12 Reactome WNT5A-dependent internalization of FZD4 Signal Transduction 6.48e-02 3.22e-16 Reactome Nef mediated downregulation of MHC class I complex cell surface expression Disease 6.05e-02 6.78e-28 Reactome Lysosome Vesicle Biogenesis Vesicle-mediated transport 5.92e-02 3.82e-11 GO low-density lipoprotein particle receptor catabolic process biological_process 5.26e-02 3.82e-11 Reactome VLDLR internalisation and degradation Transport of small molecules 4.08e-02 3.08e-12 GO anterograde synaptic vesicle transport biological_process 3.67e-02 4.00e-36 Reactome Clathrin derived vesicle budding Vesicle-mediated transport 3.67e-02 4.00e-36 Reactome trans-Golgi Network Vesicle Budding Vesicle-mediated transport 3.24e-02 3.84e-22 GO regulation of defense response to virus by virus biological_process 2.85e-02 1.73e-13 GO clathrin binding molecular_function 2.72e-02 9.83e-21 Reactome Cargo recognition for clathrin-mediated endocytosis Vesicle-mediated transport 3.83e-03 3.28e-13 GO clathrin-dependent endocytosis 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 0e+00 0e+00 endocytosis 0e+00 0e+00 microtubule-based movement 0e+00 0e+00 antigen processing and presentation of peptide antigen via MHC class II 0e+00 0e+00 regulation of viral process 0e+00 0e+00 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 0e+00 0e+00 regulation of defense response to virus by virus 0e+00 0e+00 antigen processing and presentation of peptide antigen 0e+00 0e+00 endosomal transport 0e+00 0e+00 antigen processing and presentation 0e+00 0e+00 antigen processing and presentation of exogenous peptide antigen via MHC class II 0e+00 0e+00 regulation of defense response to virus 0e+00 0e+00 clathrin coat 0e+00 0e+00 membrane coat 0e+00 0e+00 AP-type membrane coat adaptor complex 0e+00 0e+00 clathrin adaptor complex 0e+00 0e+00 vesicle coat 0e+00 0e+00 clathrin-coated vesicle 0e+00 0e+00 clathrin vesicle coat 0e+00 0e+00 coated vesicle 0e+00 0e+00 clathrin-coated vesicle membrane

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 MHC CLASS II ANTIGEN PRESENTATION 0.00e+00 0.00e+00 TRANS GOLGI NETWORK VESICLE BUDDING 0.00e+00 0.00e+00 GOLGI ASSOCIATED VESICLE BIOGENESIS 0.00e+00 0.00e+00 NEF MEDIATES DOWN MODULATION OF CELL SURFACE RECEPTORS BY RECRUITING THEM TO CLATHRIN ADAPTERS 0.00e+00 0.00e+00 MEMBRANE TRAFFICKING 0.00e+00 0.00e+00 THE ROLE OF NEF IN HIV1 REPLICATION AND DISEASE PATHOGENESIS 0.00e+00 0.00e+00 MHC CLASS II ANTIGEN PRESENTATION 0.00e+00 0.00e+00 TRANS GOLGI NETWORK VESICLE BUDDING 0.00e+00 0.00e+00 GOLGI ASSOCIATED VESICLE BIOGENESIS 0.00e+00 0.00e+00 NEF MEDIATES DOWN MODULATION OF CELL SURFACE RECEPTORS BY RECRUITING THEM TO CLATHRIN ADAPTERS 0.00e+00 0.00e+00 MEMBRANE TRAFFICKING 0.00e+00 0.00e+00 THE ROLE OF NEF IN HIV1 REPLICATION AND DISEASE PATHOGENESIS 3.99e-13 1.57e-10 NEF MEDIATED DOWNREGULATION OF MHC CLASS I COMPLEX CELL SURFACE EXPRESSION 2.21e-11 8.39e-09 LYSOSOME VESICLE BIOGENESIS 2.53e-11 7.28e-09 NEF MEDIATED DOWNREGULATION OF MHC CLASS I COMPLEX CELL SURFACE EXPRESSION 8.60e-11 2.37e-08 LYSOSOME VESICLE BIOGENESIS 6.64e-09 1.98e-06 HOST INTERACTIONS OF HIV FACTORS 1.02e-08 2.24e-06 HOST INTERACTIONS OF HIV FACTORS 3.63e-08 9.90e-06 RETROGRADE NEUROTROPHIN SIGNALLING 4.36e-08 8.89e-06 RETROGRADE NEUROTROPHIN SIGNALLING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.89e-05 1.40e-01 partial neonatal lethality 4.52e-04 5.70e-01 decreased birth weight 5.49e-04 6.42e-01 abnormal synaptic vesicle recycling 5.70e-04 6.57e-01 hypoglycemia 6.12e-04 6.82e-01 abnormal synaptic vesicle morphology 1.27e-03 1.00e+00 abnormal circulating enzyme level 2.00e-03 1.00e+00 abnormal synaptic vesicle number 2.16e-03 1.00e+00 slow postnatal weight gain 3.77e-03 1.00e+00 increased fetal weight 5.63e-03 1.00e+00 abnormal platelet dense granule morphology 7.51e-03 1.00e+00 increased birth body size 7.52e-03 1.00e+00 decreased platelet ADP level 7.52e-03 1.00e+00 absent endometrial glands 7.52e-03 1.00e+00 abnormal uterine horn morphology 9.37e-03 1.00e+00 abnormal fatty acid oxidation 9.38e-03 1.00e+00 decreased lysosomal enzyme secretion 9.38e-03 1.00e+00 decreased platelet ATP level 9.38e-03 1.00e+00 heart hemorrhage 1.04e-02 1.00e+00 female infertility 1.12e-02 1.00e+00 abnormal platelet dense granule number

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

²FDR corrected p-value (Benjamini-Hochberg)