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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod113

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod113 Module size 47 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 65057 ACD ACD, shelterin complex subunit and telomerase recruitment factor 728113 ANXA8L2 annexin A8 like 1 64897 C12orf43 chromosome 12 open reading frame 43 90416 C15orf57 coiled-coil domain containing 32 339804 C2orf74 chromosome 2 open reading frame 74 1427 CRYGS crystallin gamma S 80169 CTC1 CST telomere replication complex component 1 1539 CYLC2 cylicin 2 116224 FAM122A family with sequence similarity 122A 9715 FAM131B family with sequence similarity 131 member B 10473 HMGN4 high mobility group nucleosomal binding domain 4 126306 JSRP1 junctional sarcoplasmic reticulum protein 1 29094 LGALSL galectin like 4001 LMNB1 lamin B1 126364 LRRC25 leucine rich repeat containing 25 4501 MT1X metallothionein 1X 115861 NXNL1 nucleoredoxin like 1 203569 PAGE2 PAGE family member 2 90737 PAGE5 PAGE family member 5 5121 PCP4 Purkinje cell protein 4 25913 POT1 protection of telomeres 1 255426 RASGEF1C RasGEF domain family member 1C 9985 REC8 REC8 meiotic recombination protein 90507 SCRN2 secernin 2 128646 SIRPD signal regulatory protein delta 10734 STAG3 stromal antigen 3 23353 SUN1 Sad1 and UNC84 domain containing 1 25777 SUN2 Sad1 and UNC84 domain containing 2 93426 SYCE1 synaptonemal complex central element protein 1 256126 SYCE2 synaptonemal complex central element protein 2 6847 SYCP1 synaptonemal complex protein 1 10388 SYCP2 synaptonemal complex protein 2 221711 SYCP2L synaptonemal complex protein 2 like 50511 SYCP3 synaptonemal complex protein 3 23345 SYNE1 spectrin repeat containing nuclear envelope protein 1 23224 SYNE2 spectrin repeat containing nuclear envelope protein 2 6899 TBX1 T-box 1 100134934 TEN1 TEN1, CST complex subunit 7013 TERF1 telomeric repeat binding factor 1 7014 TERF2 telomeric repeat binding factor 2 54386 TERF2IP TERF2 interacting protein 56158 TEX12 testis expressed 12 26277 TINF2 TERF1 interacting nuclear factor 2 65057 TPP1 ACD, shelterin complex subunit and telomerase recruitment factor 10626 TRIM16 tripartite motif containing 16 11078 TRIOBP TRIO and F-actin binding protein 92092 ZC3HAV1L zinc finger CCCH-type containing, antiviral 1 like

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 3.22e-01 5.42e-16 GO shelterin complex cellular_component 2.43e-01 1.43e-05 GO CST complex cellular_component 1.80e-01 2.55e-09 GO cytoskeletal anchoring at nuclear membrane biological_process 1.67e-01 2.92e-38 Reactome Meiotic synapsis Reproduction#Cell Cycle 1.54e-01 1.10e-14 GO synaptonemal complex assembly biological_process 8.72e-02 6.48e-15 GO nuclear telomere cap complex cellular_component 8.08e-02 1.66e-18 GO telomere capping biological_process 2.27e-02 1.84e-11 GO G-rich strand telomeric DNA binding molecular_function 1.27e-02 1.10e-14 GO negative regulation of telomere maintenance via telomerase 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 meiotic cell cycle 0.00e+00 0.00e+00 meiotic chromosome segregation 0.00e+00 0.00e+00 homologous chromosome segregation 0.00e+00 0.00e+00 chromosome organization involved in meiotic cell cycle 0.00e+00 0.00e+00 telomere maintenance via telomere lengthening 0.00e+00 0.00e+00 meiotic nuclear division 0.00e+00 0.00e+00 meiosis I 0.00e+00 0.00e+00 synaptonemal complex assembly 0.00e+00 0.00e+00 synapsis 0.00e+00 0.00e+00 synaptonemal complex organization 0.00e+00 0.00e+00 telosome 0.00e+00 0.00e+00 nuclear chromosome 0.00e+00 0.00e+00 nuclear telomere cap complex 0.00e+00 0.00e+00 synaptonemal complex 0.00e+00 0.00e+00 telomeric DNA binding 1.29e-12 8.88e-10 G-rich strand telomeric DNA binding 1.61e-12 1.11e-09 single-stranded telomeric DNA binding 3.44e-12 2.34e-09 sequence-specific single stranded DNA binding 5.71e-12 5.19e-09 telomere capping 6.80e-12 3.83e-09 condensed nuclear chromosome

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 CELL CYCLE 0.00e+00 0.00e+00 MEIOTIC SYNAPSIS 0.00e+00 0.00e+00 CHROMOSOME MAINTENANCE 0.00e+00 0.00e+00 MEIOSIS 0.00e+00 0.00e+00 MEIOTIC SYNAPSIS 0.00e+00 0.00e+00 CHROMOSOME MAINTENANCE 0.00e+00 0.00e+00 MEIOSIS 1.73e-10 4.62e-08 PACKAGING OF TELOMERE ENDS 5.97e-10 2.01e-07 PACKAGING OF TELOMERE ENDS 1.99e-09 4.67e-07 TELOMERE MAINTENANCE 2.84e-09 8.79e-07 TELOMERE MAINTENANCE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.00e-08 9.62e-04 abnormal female meiosis 7.58e-08 1.13e-03 arrest of male meiosis 7.49e-07 7.10e-03 azoospermia 3.48e-06 2.23e-02 abnormal male meiosis 8.31e-06 4.10e-02 abnormal telomere length 8.41e-06 4.14e-02 small ovary 4.39e-05 1.31e-01 absent oocytes 1.03e-04 2.31e-01 female infertility 1.90e-04 3.37e-01 absent ovarian follicles 4.89e-04 5.99e-01 abnormal gametogenesis 7.44e-04 7.62e-01 decreased testis weight 1.18e-03 9.89e-01 abnormal chromosome pairing during meiosis 1.47e-03 1.00e+00 small seminiferous tubules 1.86e-03 1.00e+00 abnormal synaptonemal complex 3.72e-03 1.00e+00 decreased mature ovarian follicle number 3.77e-03 1.00e+00 abnormal fourth pharyngeal arch morphology 3.77e-03 1.00e+00 absent ultimobranchial body 4.72e-03 1.00e+00 abnormal female reproductive system morphology 4.81e-03 1.00e+00 impaired exercise endurance 5.65e-03 1.00e+00 cervical aortic arch

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

²FDR corrected p-value (Benjamini-Hochberg)