Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod198

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod198 Module size 80 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 691416 AKNA AKNA domain containing 1 6311 ATXN2 ataxin 2 11273 ATXN2L ataxin 2 like 599 BCL2L2 BCL2 like 2 100529063 BCL2L2-PABPN1 BCL2L2-PABPN1 readthrough 80114 BICC1 BicC family RNA binding protein 1 4076 CAPRIN1 cell cycle associated protein 1 65981 CAPRIN2 caprin family member 2 23589 CARHSP1 calcium regulated heat stable protein 1 7555 CNBP CCHC-type zinc finger nucleic acid binding protein 27254 CSDC2 cold shock domain containing C2 196513 DCP1B decapping mRNA 1B 55308 DDX19A DEAD-box helicase 19A 11269 DDX19B DEAD-box helicase 19B 29118 DDX25 DEAD-box helicase 25 10212 DDX39A DExD-box helicase 39A 7919 DDX39B DExD-box helicase 39B 1654 DDX3X DEAD-box helicase 3 X-linked 8653 DDX3Y DEAD-box helicase 3 Y-linked 54514 DDX4 DEAD-box helicase 4 51428 DDX41 DEAD-box helicase 41 11325 DDX42 DEAD-box helicase 42 55510 DDX43 DEAD-box helicase 43 9879 DDX46 DEAD-box helicase 46 168400 DDX53 DEAD-box helicase 53 253314 EIF4E1B eukaryotic translation initiation factor 4E family member 1B 9470 EIF4E2 eukaryotic translation initiation factor 4E family member 2 317649 EIF4E3 eukaryotic translation initiation factor 4E family member 3 8672 EIF4G3 eukaryotic translation initiation factor 4 gamma 3 83640 FAM103A1 RNA guanine-7 methyltransferase activating subunit 2218 FKTN fukutin 2332 FMR1 fragile X mental retardation 1 10146 G3BP1 G3BP stress granule assembly factor 1 9908 G3BP2 G3BP stress granule assembly factor 2 64599 GIGYF1 GRB10 interacting GYF protein 1 26058 GIGYF2 GRB10 interacting GYF protein 2 9931 HELZ helicase with zinc finger 389421 LIN28B lin-28 homolog B 26065 LSM14A LSM14A, mRNA processing body assembly factor 149986 LSM14B LSM family member 14B 57409 MIF4GD MIF4G domain containing 100500804 MIR3654 microRNA 3654 54456 MOV10L1 Mov10 like RISC complex RNA helicase 1 55149 MTPAP mitochondrial poly(A) polymerase 50804 MYEF2 myelin expression factor 2 80336 PABPC1L poly(A) binding protein cytoplasmic 1 like 340529 PABPC1L2A poly(A) binding protein cytoplasmic 1 like 2A 645974 PABPC1L2B poly(A) binding protein cytoplasmic 1 like 2B 5042 PABPC3 poly(A) binding protein cytoplasmic 3 8761 PABPC4 poly(A) binding protein cytoplasmic 4 132430 PABPC4L poly(A) binding protein cytoplasmic 4 like 140886 PABPC5 poly(A) binding protein cytoplasmic 5 390748 PABPN1L poly(A) binding protein nuclear 1 like, cytoplasmic 167153 PAPD4 terminal nucleotidyltransferase 2 64282 PAPD5 terminal nucleotidyltransferase 4B 11044 PAPD7 terminal nucleotidyltransferase 4A 9271 PIWIL1 piwi like RNA-mediated gene silencing 1 55124 PIWIL2 piwi like RNA-mediated gene silencing 2 440822 PIWIL3 piwi like RNA-mediated gene silencing 3 143689 PIWIL4 piwi like RNA-mediated gene silencing 4 84271 POLDIP3 DNA polymerase delta interacting protein 3 29890 RBM15B RNA binding motif protein 15B 5939 RBMS2 RNA binding motif single stranded interacting protein 2 56163 RNF17 ring finger protein 17 57466 SCAF4 SR-related CTD associated factor 4 22828 SCAF8 SR-related CTD associated factor 8 23064 SETX senataxin 1317 SLC31A1 solute carrier family 31 member 1 7072 TIA1 TIA1 cytotoxic granule associated RNA binding protein 7073 TIAL1 TIA1 cytotoxic granule associated RNA binding protein like 1 64852 TUT1 terminal uridylyl transferase 1, U6 snRNA-specific 79713 U2AF1L4 IGF like family receptor 1 51087 YBX2 Y-box binding protein 2 54915 YTHDF1 YTH N6-methyladenosine RNA binding protein 1 51441 YTHDF2 YTH N6-methyladenosine RNA binding protein 2 79882 ZC3H14 zinc finger CCCH-type containing 14 23318 ZCCHC11 terminal uridylyl transferase 4 389874 ZCCHC13 zinc finger CCHC-type containing 13 79670 ZCCHC6 terminal uridylyl transferase 7 196441 ZFC3H1 zinc finger C3H1-type containing

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 2.91e-01 6.23e-11 GO polynucleotide adenylyltransferase activity molecular_function 2.69e-01 2.82e-07 GO RNA uridylyltransferase activity molecular_function 2.44e-01 7.35e-12 GO P granule cellular_component 2.28e-01 7.35e-12 GO mRNA cap binding complex cellular_component 2.19e-01 9.57e-19 GO poly(A) binding molecular_function 1.37e-01 1.06e-13 GO histone mRNA catabolic process biological_process 1.20e-01 7.71e-26 GO cytoplasmic stress granule cellular_component 9.51e-02 3.10e-10 GO ATP-dependent RNA helicase activity molecular_function 8.19e-02 2.44e-06 GO miRNA catabolic process biological_process 7.62e-02 3.27e-09 GO stress granule assembly biological_process 7.56e-02 3.59e-04 GO N6-methyladenosine-containing RNA binding molecular_function 4.84e-02 5.58e-14 GO regulation of translation biological_process 3.20e-02 1.86e-13 GO poly(U) RNA binding molecular_function 2.91e-02 8.31e-07 GO negative regulation of transposition biological_process 2.70e-02 3.27e-09 GO piRNA metabolic process biological_process 1.11e-02 1.31e-06 GO oocyte maturation 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 regulation of translation 0.00e+00 0.00e+00 posttranscriptional regulation of gene expression 0.00e+00 0.00e+00 RNA secondary structure unwinding 0.00e+00 0.00e+00 ribonucleoprotein granule 0.00e+00 0.00e+00 cytoplasmic ribonucleoprotein granule 0.00e+00 0.00e+00 intracellular ribonucleoprotein complex 0.00e+00 0.00e+00 ribonucleoprotein complex 0.00e+00 0.00e+00 cytoplasmic stress granule 0.00e+00 0.00e+00 RNA helicase activity 0.00e+00 0.00e+00 RNA-dependent ATPase activity 0.00e+00 0.00e+00 ATP-dependent helicase activity 0.00e+00 0.00e+00 helicase activity 0.00e+00 0.00e+00 ATP-dependent RNA helicase activity 9.15e-16 8.63e-13 mRNA metabolic process 3.79e-14 3.55e-11 mRNA processing 1.52e-11 8.43e-09 mRNA cap binding complex 2.02e-11 1.31e-08 ATPase activity, coupled 3.49e-11 1.87e-08 RNA cap binding complex 4.43e-11 3.80e-08 RNA 3'-end processing 1.76e-10 1.43e-07 histone mRNA catabolic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 4.02e-06 8.17e-04 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 8.02e-06 1.22e-03 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 1.10e-04 1.69e-02 INTERFERON SIGNALING 1.63e-04 2.40e-02 CYTOKINE SIGNALING IN IMMUNE SYSTEM 2.88e-04 3.31e-02 INTERFERON SIGNALING 6.90e-04 7.21e-02 CYTOKINE SIGNALING IN IMMUNE SYSTEM 1.60e-02 1.00e+00 MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE 2.52e-02 1.00e+00 MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE 3.14e-02 1.00e+00 METAL ION SLC TRANSPORTERS 3.51e-02 1.00e+00 DEADENYLATION DEPENDENT MRNA DECAY 3.68e-02 1.00e+00 METAL ION SLC TRANSPORTERS 4.32e-02 1.00e+00 DEADENYLATION DEPENDENT MRNA DECAY

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.36e-08 3.19e-04 abnormal male germ cell apoptosis 1.11e-07 1.52e-03 azoospermia 1.28e-07 1.69e-03 arrest of male meiosis 9.96e-07 8.76e-03 small testis 5.93e-06 3.24e-02 decreased testis weight 3.77e-05 1.18e-01 abnormal spermatocyte morphology 6.26e-05 1.65e-01 small seminiferous tubules 2.92e-04 4.42e-01 arrest of spermatogenesis 1.27e-03 1.00e+00 abnormal Reichert's membrane morphology 3.14e-03 1.00e+00 small ovary 3.42e-03 1.00e+00 decreased primordial germ cell number 4.04e-03 1.00e+00 abnormal seminiferous tubule epithelium morphology 4.53e-03 1.00e+00 ovary cysts 5.63e-03 1.00e+00 enlarged seminal vesicle 5.63e-03 1.00e+00 abnormal embryonic cilium location or orientation 7.10e-03 1.00e+00 female infertility 7.49e-03 1.00e+00 decreased brain copper level 7.49e-03 1.00e+00 abnormal copper level 8.13e-03 1.00e+00 abnormal seminiferous tubule morphology 9.35e-03 1.00e+00 absent Leydig cells

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

²FDR corrected p-value (Benjamini-Hochberg)