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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod39

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod39 Module size 48 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1434 CSE1L chromosome segregation 1 like 285381 DPH3 diphthamide biosynthesis 3 359787 DPPA3 developmental pluripotency associated 3 283450 HECTD4 HECT domain E3 ubiquitin protein ligase 4 51194 IPO11 importin 11 9670 IPO13 importin 13 79711 IPO4 importin 4 3843 IPO5 importin 5 3836 KPNA1 karyopherin subunit alpha 1 3838 KPNA2 karyopherin subunit alpha 2 3839 KPNA3 karyopherin subunit alpha 3 3840 KPNA4 karyopherin subunit alpha 4 3841 KPNA5 karyopherin subunit alpha 5 23633 KPNA6 karyopherin subunit alpha 6 402569 KPNA7 karyopherin subunit alpha 7 3837 KPNB1 karyopherin subunit beta 1 54830 NUP62CL nucleoporin 62 C-terminal like 10204 NUTF2 nuclear transport factor 2 5901 RAN RAN, member RAS oncogene family 5902 RANBP1 RAN binding protein 1 8498 RANBP3 RAN binding protein 3 202151 RANBP3L RAN binding protein 3 like 26953 RANBP6 RAN binding protein 6 29098 RANGRF RAN guanine nucleotide release factor 55213 RCBTB1 RCC1 and BTB domain containing protein 1 1102 RCBTB2 RCC1 and BTB domain containing protein 2 308760 RCC1 RCC1 domain containing 1 91433 RCCD1 RCC1 domain containing 1 400966 RGPD1 RANBP2-like and GRIP domain containing 1 400966 RGPD2 RANBP2-like and GRIP domain containing 1 653489 RGPD3 RANBP2-like and GRIP domain containing 3 285190 RGPD4 RANBP2-like and GRIP domain containing 4 84220 RGPD5 RANBP2-like and GRIP domain containing 5 729540 RGPD6 RANBP2-like and GRIP domain containing 6 727851 RGPD8 RANBP2-like and GRIP domain containing 8 6103 RPGR retinitis pigmentosa GTPase regulator 55197 RPRD1A regulation of nuclear pre-mRNA domain containing 1A 58490 RPRD1B regulation of nuclear pre-mRNA domain containing 1B 26297 SERGEF secretion regulating guanine nucleotide exchange factor 200162 SPAG17 sperm associated antigen 17 9576 SPAG6 sperm associated antigen 6 23306 TMEM194A nuclear envelope integral membrane protein 1 100131211 TMEM194B nuclear envelope integral membrane protein 2 30000 TNPO2 transportin 2 81671 VMP1 vacuole membrane protein 1 81554 WBSCR16 RCC1 like 65249 ZSWIM4 zinc finger SWIM-type containing 4 57643 ZSWIM5 zinc finger SWIM-type containing 5

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 4.02e-01 3.47e-20 GO nuclear import signal receptor activity molecular_function 3.17e-01 6.15e-43 GO Ran GTPase binding molecular_function 2.53e-01 4.73e-40 GO NLS-bearing protein import into nucleus biological_process 1.05e-01 4.77e-15 GO ribosomal protein import into nucleus biological_process 3.04e-02 7.61e-23 GO nuclear localization sequence binding molecular_function 2.18e-02 3.32e-04 GO RNA polymerase II, holoenzyme cellular_component 1.40e-02 3.98e-04 GO negative regulation of protein secretion biological_process 3.25e-03 6.90e-30 GO nuclear pore 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 0e+00 0e+00 single-organism nuclear import 0e+00 0e+00 nuclear import 0e+00 0e+00 nuclear transport 0e+00 0e+00 nucleocytoplasmic transport 0e+00 0e+00 protein import into nucleus, translocation 0e+00 0e+00 modulation by virus of host morphology or physiology 0e+00 0e+00 protein localization to nucleus 0e+00 0e+00 ribosomal protein import into nucleus 0e+00 0e+00 protein targeting 0e+00 0e+00 protein import into nucleus 0e+00 0e+00 NLS-bearing protein import into nucleus 0e+00 0e+00 protein localization to organelle 0e+00 0e+00 establishment of protein localization to organelle 0e+00 0e+00 modulation by virus of host process 0e+00 0e+00 protein import 0e+00 0e+00 nuclear envelope 0e+00 0e+00 nuclear pore 0e+00 0e+00 peptide transporter activity 0e+00 0e+00 protein transporter activity 0e+00 0e+00 peptide binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.29e-11 1.24e-08 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 1.73e-09 4.11e-07 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 5.13e-09 1.54e-06 HOST INTERACTIONS OF HIV FACTORS 5.07e-08 1.36e-05 INTERFERON SIGNALING 1.39e-07 3.53e-05 HIV INFECTION 4.36e-07 1.04e-04 CYTOKINE SIGNALING IN IMMUNE SYSTEM 6.53e-07 1.17e-04 INTERFERON SIGNALING 1.74e-06 2.92e-04 HOST INTERACTIONS OF HIV FACTORS 7.43e-06 1.14e-03 CYTOKINE SIGNALING IN IMMUNE SYSTEM 1.18e-05 2.23e-03 TRANSPORT OF RIBONUCLEOPROTEINS INTO THE HOST NUCLEUS 2.25e-05 3.18e-03 HIV INFECTION 3.93e-05 6.75e-03 INFLUENZA LIFE CYCLE 6.33e-05 1.03e-02 LATE PHASE OF HIV LIFE CYCLE 1.30e-04 1.97e-02 HIV LIFE CYCLE 2.22e-04 2.61e-02 INFLUENZA LIFE CYCLE 4.66e-04 6.05e-02 APOPTOSIS INDUCED DNA FRAGMENTATION 6.22e-04 6.57e-02 APOPTOSIS INDUCED DNA FRAGMENTATION 1.08e-03 1.08e-01 TRANSPORT OF RIBONUCLEOPROTEINS INTO THE HOST NUCLEUS 1.20e-03 1.18e-01 LATE PHASE OF HIV LIFE CYCLE 1.63e-03 1.55e-01 HIV LIFE CYCLE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 0.00e+00 0.00e+00 elevated level of mitotic sister chromatid exchange 2.66e-12 1.98e-07 decreased tumor latency 7.84e-11 4.42e-06 increased lung carcinoma incidence 1.36e-10 7.46e-06 abnormal rod electrophysiology 9.74e-10 3.76e-05 increased sarcoma incidence 1.02e-09 3.80e-05 abnormal mitosis 1.81e-09 5.70e-05 aneuploidy 6.04e-09 1.68e-04 increased incidence of tumors by chemical induction 1.19e-08 2.91e-04 increased hepatocellular carcinoma incidence 1.30e-08 3.08e-04 abnormal nervous system physiology 1.99e-08 4.11e-04 decreased susceptibility to diet-induced obesity 3.67e-08 6.54e-04 complete prenatal lethality 3.89e-08 6.78e-04 increased tumor incidence 1.34e-07 1.75e-03 impaired glucose tolerance 1.56e-06 1.20e-02 complete embryonic lethality 2.04e-06 1.49e-02 complete preweaning lethality 1.87e-03 1.00e+00 abnormal pulmonary alveolus epithelium morphology 3.75e-03 1.00e+00 abnormal pregnancy 3.75e-03 1.00e+00 absent sperm head 5.61e-03 1.00e+00 neural tube degeneration

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

²FDR corrected p-value (Benjamini-Hochberg)