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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod104

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod104 Module size 43 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 8125 ANP32A acidic nuclear phosphoprotein 32 family member A 10541 ANP32B acidic nuclear phosphoprotein 32 family member B 23519 ANP32D acidic nuclear phosphoprotein 32 family member D 55909 BIN3 bridging integrator 3 29080 CCDC59 coiled-coil domain containing 59 2079 ERH ERH, mRNA splicing and mitosis factor NA FAM197Y1 3005 H1F0 H1 histone family member 0 132243 H1FOO H1 histone family member O oocyte specific 8971 H1FX H1 histone family member X 3015 H2AFZ H2A histone family member Z 3024 HIST1H1A histone cluster 1 H1 family member a 3009 HIST1H1B histone cluster 1 H1 family member b 3006 HIST1H1C histone cluster 1 H1 family member c 3007 HIST1H1D histone cluster 1 H1 family member d 3008 HIST1H1E histone cluster 1 H1 family member e 3010 HIST1H1T histone cluster 1 H1 family member t 50809 HP1BP3 heterochromatin protein 1 binding protein 3 124535 HSF5 heat shock transcription factor 5 55705 IPO9 importin 9 4673 NAP1L1 nucleosome assembly protein 1 like 1 4674 NAP1L2 nucleosome assembly protein 1 like 2 4675 NAP1L3 nucleosome assembly protein 1 like 3 4676 NAP1L4 nucleosome assembly protein 1 like 4 266812 NAP1L5 nucleosome assembly protein 1 like 5 645996 NAP1L6 nucleosome assembly protein 1 like 6 9677 PPIP5K1 diphosphoinositol pentakisphosphate kinase 1 23262 PPIP5K2 diphosphoinositol pentakisphosphate kinase 2 312299 SET enhancer of zeste 2 polycomb repressive complex 2 subunit 7258 TSPY1 testis specific protein Y-linked 1 100289087 TSPY10 testis specific protein Y-linked 10 64591 TSPY2 testis specific protein Y-linked 2 728137 TSPY3 testis specific protein Y-linked 3 728395 TSPY4 testis specific protein Y-linked 4 728403 TSPY8 testis specific protein Y-linked 8 7259 TSPYL1 TSPY like 1 64061 TSPYL2 TSPY like 2 23270 TSPYL4 TSPY like 4 85453 TSPYL5 TSPY like 5 388951 TSPYL6 TSPY like 6 254173 TTLL10 tubulin tyrosine ligase like 10 340554 ZC3H12B zinc finger CCCH-type containing 12B 340152 ZC3H12D zinc finger CCCH-type containing 12D

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 2.20e-01 2.31e-59 GO nucleosome assembly biological_process 1.54e-01 5.81e-05 GO inositol hexakisphosphate kinase activity molecular_function 1.18e-01 6.17e-21 GO negative regulation of chromatin silencing biological_process 9.63e-02 2.99e-20 GO chromosome condensation biological_process 6.20e-02 1.13e-19 GO negative regulation of DNA recombination biological_process 5.43e-02 1.41e-20 GO nucleosome positioning biological_process 2.90e-02 7.32e-03 Reactome Defective pro-SFTPB causes pulmonary surfactant metabolism dysfunction 1 (SMDP1) and respiratory distress syndrome (RDS) Disease 2.03e-02 2.49e-13 Reactome Activation of DNA fragmentation factor Programmed Cell Death 2.00e-02 2.49e-13 Reactome Apoptosis induced DNA fragmentation Programmed Cell Death 1.13e-02 2.59e-04 Reactome HuR (ELAVL1) binds and stabilizes mRNA Metabolism of RNA 6.48e-03 1.35e-13 Reactome Formation of Senescence-Associated Heterochromatin Foci (SAHF) Cellular responses to external stimuli

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 nucleosome organization 0.00e+00 0.00e+00 protein-DNA complex assembly 0.00e+00 0.00e+00 chromatin assembly 0.00e+00 0.00e+00 chromatin assembly or disassembly 0.00e+00 0.00e+00 DNA conformation change 0.00e+00 0.00e+00 chromatin organization 0.00e+00 0.00e+00 DNA packaging 0.00e+00 0.00e+00 nucleosome assembly 0.00e+00 0.00e+00 protein-DNA complex 0.00e+00 0.00e+00 nucleosome 0.00e+00 0.00e+00 chromatin DNA binding 1.01e-10 8.37e-08 gonadal mesoderm development 2.12e-10 1.05e-07 chromatin 2.59e-10 1.51e-07 chromatin binding 1.89e-09 8.23e-07 nuclear euchromatin 5.52e-09 2.26e-06 euchromatin 1.10e-07 6.18e-05 mesoderm development 1.36e-07 7.51e-05 mesenchyme development 3.40e-07 1.76e-04 nucleosome positioning 9.95e-07 4.73e-04 gonad development

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 APOPTOSIS INDUCED DNA FRAGMENTATION 0.00e+00 0.00e+00 APOPTOSIS INDUCED DNA FRAGMENTATION 3.86e-11 1.44e-08 APOPTOTIC EXECUTION PHASE 2.48e-10 6.50e-08 APOPTOTIC EXECUTION PHASE 3.05e-10 1.06e-07 APOPTOSIS 5.67e-08 1.14e-05 APOPTOSIS 2.95e-02 1.00e+00 REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU RICH ELEMENTS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.74e-03 1e+00 increased T-helper 17 cell number 5.61e-03 1e+00 increased incidence of tumors by ionizing radiation induction 9.35e-03 1e+00 increased interleukin-10 secretion 9.37e-03 1e+00 partial lethality 1.50e-02 1e+00 increased lung adenocarcinoma incidence 1.50e-02 1e+00 abnormal lens fiber morphology 1.62e-02 1e+00 abnormal cell cycle checkpoint function 1.68e-02 1e+00 increased susceptibility to experimental autoimmune encephalomyelitis 1.69e-02 1e+00 extramedullary hematopoiesis 1.81e-02 1e+00 decreased heart weight 1.94e-02 1e+00 increased lymphoma incidence 2.05e-02 1e+00 abnormal inner cell mass morphology 2.07e-02 1e+00 liver inflammation 2.26e-02 1e+00 lung inflammation 2.43e-02 1e+00 increased interleukin-6 secretion 2.43e-02 1e+00 increased CD8-positive, alpha-beta T cell number 2.48e-02 1e+00 complete embryonic lethality between implantation and somite formation 2.75e-02 1e+00 abnormal hepatocyte morphology 2.75e-02 1e+00 increased blood urea nitrogen level 3.03e-02 1e+00 decreased bone mineral density

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

²FDR corrected p-value (Benjamini-Hochberg)