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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod35

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod35 Module size 50 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 283847 CCDC79 telomere repeat binding bouquet formation protein 1 163126 EID2 EP300 interacting inhibitor of differentiation 2 126272 EID2B EP300 interacting inhibitor of differentiation 2B 493861 EID3 EP300 interacting inhibitor of differentiation 3 4100 MAGEA1 MAGE family member A1 4109 MAGEA10 MAGE family member A10 4110 MAGEA11 MAGE family member A11 4111 MAGEA12 MAGE family member A12 266740 MAGEA2 MAGE family member A2B 266740 MAGEA2B MAGE family member A2B 4102 MAGEA3 MAGE family member A3 4104 MAGEA4 MAGE family member A5 4102 MAGEA6 MAGE family member A3 4107 MAGEA8 MAGE family member A8 4108 MAGEA9 MAGE family member A9 728269 MAGEA9B MAGE family member A9B 4112 MAGEB1 MAGE family member B1 139422 MAGEB10 MAGE family member B10 139604 MAGEB16 MAGE family member B16 645864 MAGEB17 MAGE family member B17 286514 MAGEB18 MAGE family member B18 4113 MAGEB2 MAGE family member B2 4114 MAGEB3 MAGE family member B3 4115 MAGEB4 MAGE family member B4 347541 MAGEB5 MAGE family member B5 158809 MAGEB6 MAGE family member B6 9947 MAGEC1 MAGE family member C1 51438 MAGEC2 MAGE family member C2 139081 MAGEC3 MAGE family member C3 9500 MAGED1 MAGE family member D1 10916 MAGED2 MAGE family member D2 728239 MAGED4 MAGE family member D4 81557 MAGED4B MAGE family member D4B 139599 MAGEE2 MAGE family member E2 64110 MAGEF1 MAGE family member F1 28986 MAGEH1 MAGE family member H1 54551 MAGEL2 MAGE family member L2 4692 NDN necdin, MAGE family member 56160 NDNL2 NSE3 homolog, SMC5-SMC6 complex component 197370 NSMCE1 NSE1 homolog, SMC5-SMC6 complex component 286053 NSMCE2 NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase 54780 NSMCE4A NSE4 homolog A, SMC5-SMC6 complex component 22976 PAXIP1 PAX interacting protein 1 8243 SMC1A structural maintenance of chromosomes 1A 27127 SMC1B structural maintenance of chromosomes 1B 83452 SMC2 RAB33B, member RAS oncogene family 10051 SMC4 structural maintenance of chromosomes 4 23137 SMC5 structural maintenance of chromosomes 5 79677 SMC6 structural maintenance of chromosomes 6 7216 TRO trophinin

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 5.77e-01 1.98e-17 GO Smc5-Smc6 complex cellular_component 7.91e-02 3.59e-05 GO condensin complex cellular_component 4.33e-02 8.01e-10 GO positive regulation of response to DNA damage stimulus biological_process 3.23e-03 2.36e-06 GO sister chromatid cohesion biological_process 2.28e-03 1.55e-04 GO cellular protein catabolic process 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 0.00e+00 0.00e+00 condensed chromosome 0.00e+00 0.00e+00 Smc5-Smc6 complex 1.76e-08 1.11e-05 DNA recombination 2.38e-08 1.48e-05 cellular senescence 4.69e-08 1.70e-05 chromosome, telomeric region 3.94e-07 2.01e-04 DNA repair 4.71e-07 2.38e-04 cell aging 2.43e-06 1.07e-03 positive regulation of chromosome segregation 3.02e-06 1.31e-03 double-strand break repair 3.21e-06 1.38e-03 cellular response to DNA damage stimulus 5.35e-06 2.20e-03 sister chromatid segregation 9.21e-06 3.59e-03 double-strand break repair via homologous recombination 9.22e-06 3.60e-03 recombinational repair 1.17e-05 4.46e-03 DNA metabolic process 1.87e-05 6.78e-03 telomere maintenance via recombination 1.93e-05 6.96e-03 positive regulation of maintenance of mitotic sister chromatid cohesion 2.40e-05 5.46e-03 PML body 3.46e-05 1.16e-02 mitotic recombination 4.15e-05 1.37e-02 double-strand break repair via nonhomologous end joining 4.49e-05 9.60e-03 nuclear body

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.26e-04 2.65e-02 MEIOTIC SYNAPSIS 4.72e-04 5.15e-02 CHROMOSOME MAINTENANCE 2.12e-03 1.96e-01 MEIOSIS 3.16e-03 3.15e-01 MEIOTIC SYNAPSIS 4.68e-03 4.33e-01 CHROMOSOME MAINTENANCE 5.15e-03 4.69e-01 ROLE OF DCC IN REGULATING APOPTOSIS 5.18e-03 4.70e-01 REGULATION OF APOPTOSIS 6.22e-03 5.47e-01 MEIOSIS 1.05e-02 7.62e-01 ROLE OF DCC IN REGULATING APOPTOSIS 1.14e-02 8.16e-01 REGULATION OF APOPTOSIS 2.82e-02 1.00e+00 CELL CYCLE 3.91e-02 1.00e+00 NRAGE SIGNALS DEATH THROUGH JNK 4.55e-02 1.00e+00 NRAGE SIGNALS DEATH THROUGH JNK 4.60e-02 1.00e+00 APOPTOSIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.45e-04 2.90e-01 maternal imprinting 5.98e-04 6.73e-01 abnormal circadian rhythm 1.87e-03 1.00e+00 abnormal female meiosis I arrest 1.87e-03 1.00e+00 increased cellular sensitivity to methylmethanesulfonate 2.58e-03 1.00e+00 abnormal female meiosis 3.05e-03 1.00e+00 abnormal male meiosis 3.74e-03 1.00e+00 anhedonia 3.74e-03 1.00e+00 decreased serotonin level 4.37e-03 1.00e+00 increased thermal nociceptive threshold 5.61e-03 1.00e+00 ovary degeneration 5.61e-03 1.00e+00 abnormal X-Y chromosome synapsis during male meiosis 5.61e-03 1.00e+00 abnormal hair cycle catagen phase 7.47e-03 1.00e+00 increased serotonin level 7.47e-03 1.00e+00 abnormal superior cervical ganglion morphology 7.47e-03 1.00e+00 abnormal hypothalamus secretion 7.47e-03 1.00e+00 hypoventilation 8.23e-03 1.00e+00 arrest of male meiosis 9.58e-03 1.00e+00 abnormal male germ cell apoptosis 1.06e-02 1.00e+00 azoospermia 1.12e-02 1.00e+00 impaired olfaction

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

²FDR corrected p-value (Benjamini-Hochberg)