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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod324

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod324 Module size 39 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10973 ASCC3 activating signal cointegrator 1 complex subunit 3 295334 BCAS2 BCAS2, pre-mRNA processing factor 8896 BUD31 BUD31 homolog 83938 C10orf11 leucine rich melanocyte differentiation associated 151903 CCDC12 coiled-coil domain containing 12 55702 CCDC94 YJU2 splicing factor homolog 988 CDC5L cell division cycle 5 like 51340 CRNKL1 crooked neck pre-mRNA splicing factor 1 57703 CWC22 CWC22 spliceosome associated protein homolog 360613 CWC25 CWC25 spliceosome-associated protein homolog 1665 DHX15 DEAH-box helicase 15 8449 DHX16 DEAH-box helicase 16 54505 DHX29 DExH-box helicase 29 22907 DHX30 DExH-box helicase 30 55760 DHX32 DEAH-box helicase 32 (putative) 56919 DHX33 DEAH-box helicase 33 9704 DHX34 DExH-box helicase 34 60625 DHX35 DEAH-box helicase 35 170506 DHX36 DEAH-box helicase 36 79665 DHX40 DEAH-box helicase 40 90957 DHX57 DExH-box helicase 57 1659 DHX8 DEAH-box helicase 8 165545 DQX1 DEAQ-box RNA dependent ATPase 1 113510 HELQ helicase, POLQ like 164045 HFM1 HFM1, ATP dependent DNA helicase homolog 57461 ISY1 ISY1 splicing factor homolog 100534599 ISY1-RAB43 ISY1-RAB43 readthrough 5356 PLRG1 pleiotropic regulator 1 8559 PRPF18 pre-mRNA processing factor 18 27339 PRPF19 pre-mRNA processing factor 19 55696 RBM22 RNA binding motif protein 22 163859 SDE2 SDE2 telomere maintenance homolog 22938 SNW1 SNW domain containing 1 222183 SRRM3 serine/arginine repetitive matrix 3 170933 SYF2 SYF2 pre-mRNA-splicing factor 24144 TFIP11 tuftelin interacting protein 11 56949 XAB2 XPA binding protein 2 64848 YTHDC2 YTH domain containing 2 51538 ZCCHC17 zinc finger CCHC-type containing 17

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 5.58e-01 1.21e-35 GO ATP-dependent 3'-5' RNA helicase activity molecular_function 3.62e-01 3.92e-22 GO Prp19 complex cellular_component 1.70e-01 3.09e-26 GO U2-type catalytic step 2 spliceosome 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 0.00e+00 0.00e+00 RNA splicing, via transesterification reactions 0.00e+00 0.00e+00 RNA splicing 0.00e+00 0.00e+00 mRNA metabolic process 0.00e+00 0.00e+00 mRNA processing 0.00e+00 0.00e+00 mRNA splicing, via spliceosome 0.00e+00 0.00e+00 catalytic step 2 spliceosome 0.00e+00 0.00e+00 intracellular ribonucleoprotein complex 0.00e+00 0.00e+00 spliceosomal complex 0.00e+00 0.00e+00 ribonucleoprotein complex 0.00e+00 0.00e+00 Prp19 complex 0.00e+00 0.00e+00 ATPase activity 0.00e+00 0.00e+00 nucleoside-triphosphatase 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 ATPase activity, coupled 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 RNA helicase activity 1.69e-11 9.30e-09 post-mRNA release spliceosomal complex 1.40e-10 7.07e-08 catalytic step 1 spliceosome

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.37e-03 3.31e-01 FORMATION OF TRANSCRIPTION COUPLED NER TC NER REPAIR COMPLEX 3.38e-03 3.32e-01 TRANSCRIPTION COUPLED NER TC NER 8.33e-03 6.93e-01 NUCLEOTIDE EXCISION REPAIR 8.64e-03 6.53e-01 FORMATION OF TRANSCRIPTION COUPLED NER TC NER REPAIR COMPLEX 8.67e-03 6.55e-01 TRANSCRIPTION COUPLED NER TC NER 9.00e-03 6.75e-01 NOTCH HLH TRANSCRIPTION PATHWAY 1.03e-02 8.15e-01 NOTCH HLH TRANSCRIPTION PATHWAY 1.42e-02 9.73e-01 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 1.67e-02 1.00e+00 NUCLEOTIDE EXCISION REPAIR 1.68e-02 1.00e+00 PRE NOTCH TRANSCRIPTION AND TRANSLATION 1.97e-02 1.00e+00 SIGNALING BY NOTCH1 2.02e-02 1.00e+00 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 2.18e-02 1.00e+00 PRE NOTCH EXPRESSION AND PROCESSING 2.26e-02 1.00e+00 PRE NOTCH TRANSCRIPTION AND TRANSLATION 2.27e-02 1.00e+00 PRE NOTCH EXPRESSION AND PROCESSING 3.03e-02 1.00e+00 SIGNALING BY NOTCH1 3.34e-02 1.00e+00 SIGNALING BY NOTCH 4.67e-02 1.00e+00 SIGNALING BY NOTCH

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.88e-04 3.35e-01 abnormal ovary morphology 8.68e-04 8.33e-01 complete embryonic lethality before implantation 1.87e-03 1.00e+00 abnormal X-Y chromosome synapsis during male meiosis 3.74e-03 1.00e+00 increased gland tumor incidence 3.75e-03 1.00e+00 increased ovary tumor incidence 5.61e-03 1.00e+00 increased pituitary adenoma incidence 5.62e-03 1.00e+00 ovary atrophy 5.62e-03 1.00e+00 abnormal ovarian follicle number 5.62e-03 1.00e+00 decreased corpora lutea number 7.47e-03 1.00e+00 abnormal chiasmata formation 7.48e-03 1.00e+00 increased NK T cell number 7.49e-03 1.00e+00 abnormal oogenesis 7.50e-03 1.00e+00 absent mature ovarian follicles 9.15e-03 1.00e+00 decreased cell proliferation 9.34e-03 1.00e+00 long tibia 9.34e-03 1.00e+00 abnormal synaptonemal complex 9.34e-03 1.00e+00 abnormal meiosis 9.36e-03 1.00e+00 ovary cysts 1.06e-02 1.00e+00 increased mammary gland tumor incidence 1.12e-02 1.00e+00 abnormal chromosome pairing during meiosis

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

²FDR corrected p-value (Benjamini-Hochberg)