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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod73

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod73 Module size 52 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 83734 ATG10 autophagy related 10 9140 ATG12 autophagy related 12 362164 ATG13 autophagy related 13 89849 ATG16L2 autophagy related 16 like 2 23130 ATG2A autophagy related 2A 55102 ATG2B autophagy related 2B 64422 ATG3 autophagy related 3 115201 ATG4A autophagy related 4A cysteine peptidase 23192 ATG4B autophagy related 4B cysteine peptidase 84938 ATG4C autophagy related 4C cysteine peptidase 84971 ATG4D autophagy related 4D cysteine peptidase 9474 ATG5 autophagy related 5 10533 ATG7 autophagy related 7 79065 ATG9A autophagy related 9A 284697 BTBD8 BTB domain containing 8 60673 C12orf44 autophagy related 101 64771 C6orf106 chromosome 6 open reading frame 106 221322 C6orf170 TBC1 domain family member 32 22898 DENND3 DENN domain containing 3 84173 ELMOD3 ELMO domain containing 3 79137 FAM134A reticulophagy regulator family member 2 139341 FUNDC1 FUN14 domain containing 1 11337 GABARAP GABA type A receptor-associated protein 23710 GABARAPL1 GABA type A receptor associated protein like 1 11345 GABARAPL2 GABA type A receptor associated protein like 2 23766 GABARAPL3 GABA type A receptor associated protein like 3 pseudogene 474344 GIMAP6 GTPase, IMAP family member 6 126298 IRGQ immunity related GTPase Q 3891 KRT85 keratin 85 84557 MAP1LC3A microtubule associated protein 1 light chain 3 alpha 81631 MAP1LC3B microtubule associated protein 1 light chain 3 beta 643246 MAP1LC3B2 microtubule associated protein 1 light chain 3 beta 2 440738 MAP1LC3C microtubule associated protein 1 light chain 3 gamma 10198 MPHOSPH9 M-phase phosphoprotein 9 4077 NBR1 NBR1, autophagy cargo receptor 91300 R3HDM4 R3H domain containing 4 9821 RB1CC1 RB1 inducible coiled-coil 1 83667 SESN2 sestrin 2 140775 SMCR8 Smith-Magenis syndrome chromosome region, candidate 8 8878 SQSTM1 sequestosome 1 140901 STK35 serine/threonine kinase 35 26000 TBC1D10B TBC1 domain family member 10B 9895 TECPR2 tectonin beta-propeller repeat containing 2 9528 TMEM59 transmembrane protein 59 58476 TP53INP2 tumor protein p53 inducible nuclear protein 2 8408 ULK1 unc-51 like autophagy activating kinase 1 9706 ULK2 unc-51 like autophagy activating kinase 2 23001 WDFY3 WD repeat and FYVE domain containing 3 55255 WDR41 WD repeat domain 41 11152 WDR45 WD repeat domain 45 55062 WIPI1 WD repeat domain, phosphoinositide interacting 1 26100 WIPI2 WD repeat domain, phosphoinositide interacting 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 3.37e-01 6.38e-15 GO Atg1/ULK1 kinase complex cellular_component 2.23e-01 2.92e-50 GO autophagy of mitochondrion biological_process 1.66e-01 1.64e-59 GO autophagosome assembly biological_process 1.57e-01 1.48e-24 GO cellular response to nitrogen starvation biological_process 8.95e-02 1.33e-26 GO phagophore assembly site cellular_component 8.33e-02 3.97e-45 Reactome Macroautophagy Cellular responses to external stimuli 6.55e-02 1.05e-13 Reactome Receptor Mediated Mitophagy Mitophagy 6.34e-02 4.11e-23 GO phagophore assembly site membrane cellular_component 8.45e-03 1.61e-28 GO autophagy biological_process 4.83e-03 3.55e-22 GO autophagosome membrane cellular_component

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 vacuole organization 0.00e+00 0.00e+00 autophagosome organization 0.00e+00 0.00e+00 autophagosome assembly 0.00e+00 0.00e+00 autophagy 0.00e+00 0.00e+00 macroautophagy 0.00e+00 0.00e+00 organelle disassembly 0.00e+00 0.00e+00 mitophagy 0.00e+00 0.00e+00 mitochondrion organization 0.00e+00 0.00e+00 nucleophagy 0.00e+00 0.00e+00 autophagosome maturation 0.00e+00 0.00e+00 vacuole fusion 0.00e+00 0.00e+00 vacuole 0.00e+00 0.00e+00 autophagosome 0.00e+00 0.00e+00 pre-autophagosomal structure membrane 0.00e+00 0.00e+00 pre-autophagosomal structure 0.00e+00 0.00e+00 autophagosome membrane 2.95e-10 1.43e-07 vacuolar membrane 2.49e-09 1.76e-06 positive regulation of autophagy 2.59e-09 1.83e-06 protein lipidation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.78e-04 5.03e-02 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING 5.84e-04 6.22e-02 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING 1.76e-03 1.90e-01 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 2.11e-03 1.95e-01 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 3.44e-03 3.35e-01 P75NTR RECRUITS SIGNALLING COMPLEXES 3.44e-03 3.35e-01 P75NTR SIGNALS VIA NFKB 3.44e-03 3.35e-01 NFKB IS ACTIVATED AND SIGNALS SURVIVAL 3.62e-03 3.12e-01 NFKB IS ACTIVATED AND SIGNALS SURVIVAL 5.42e-03 4.39e-01 NRIF SIGNALS CELL DEATH FROM THE NUCLEUS 5.42e-03 4.39e-01 P75NTR RECRUITS SIGNALLING COMPLEXES 5.42e-03 4.39e-01 P75NTR SIGNALS VIA NFKB 1.20e-02 9.20e-01 NRIF SIGNALS CELL DEATH FROM THE NUCLEUS 1.54e-02 1.00e+00 IL1 SIGNALING 1.55e-02 1.00e+00 INNATE IMMUNE SYSTEM 1.98e-02 1.00e+00 INNATE IMMUNE SYSTEM 2.77e-02 1.00e+00 CELL DEATH SIGNALLING VIA NRAGE NRIF AND NADE 3.08e-02 1.00e+00 SIGNALING BY ILS 3.30e-02 1.00e+00 IL1 SIGNALING 3.54e-02 1.00e+00 CELL DEATH SIGNALLING VIA NRAGE NRIF AND NADE 3.90e-02 1.00e+00 P75 NTR RECEPTOR MEDIATED SIGNALLING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.45e-11 1.65e-06 abnormal autophagy 3.57e-05 1.14e-01 enlarged otoliths 7.53e-05 1.87e-01 abnormal utricle morphology 1.32e-04 2.73e-01 abnormal circulating amino acid level 1.83e-04 3.30e-01 absent otoliths 8.84e-04 8.39e-01 increased red blood cell distribution width 1.04e-03 9.21e-01 increased fibroblast apoptosis 1.71e-03 1.00e+00 abnormal osteoclast physiology 3.74e-03 1.00e+00 decreased alpha-beta T cell number 3.74e-03 1.00e+00 abnormal vestibular saccular macula morphology 3.74e-03 1.00e+00 increased diameter of humerus 3.92e-03 1.00e+00 abnormal bone ossification 5.61e-03 1.00e+00 increased osteoid thickness 5.61e-03 1.00e+00 increased diameter of femur 6.69e-03 1.00e+00 abnormal bone structure 7.47e-03 1.00e+00 decreased mitochondria number 7.48e-03 1.00e+00 neuronal intranuclear inclusions 7.63e-03 1.00e+00 abnormal hepatocyte morphology 9.33e-03 1.00e+00 dissociated hepatocytes 9.33e-03 1.00e+00 abnormal ST segment

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

²FDR corrected p-value (Benjamini-Hochberg)