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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod331

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod331 Module size 41 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 140836 BANF2 barrier to autointegration factor 2 55421 C17orf85 nuclear cap binding subunit 3 79635 CCDC121 coiled-coil domain containing 121 26097 CHTOP chromatin target of PRMT1 1207 CLNS1A chloride nucleotide-sensitive channel 1A 11218 DDX20 DEAD-box helicase 20 90459 ERI1 exoribonuclease 1 84248 FYTTD1 forty-two-three domain containing 1 9235 IL32 interleukin 32 114823 LENG8 leukocyte receptor cluster member 8 134353 LSM11 LSM11, U7 small nuclear RNA associated 1130 LYST lysosomal trafficking regulator 55110 MAGOHB mago homolog B, exon junction complex subunit 4686 NCBP1 nuclear cap binding protein subunit 1 22916 NCBP2 nuclear cap binding protein subunit 2 51070 NOSIP nitric oxide synthase interacting protein 55795 PCID2 PCI domain containing 2 5303 PIN4 peptidylprolyl cis/trans isomerase, NIMA-interacting 4 9939 RBM8A RNA binding motif protein 8A 84324 SARNP SAP domain containing ribonucleoprotein 51547 SIRT7 sirtuin 7 6606 SMN1 survival of motor neuron 1, telomeric 6607 SMN2 survival of motor neuron 2, centromeric 6636 SNRPF small nuclear ribonucleoprotein polypeptide F 26206 SPAG8 sperm associated antigen 8 51593 SRRT serrate, RNA effector molecule 153443 STRAP serum response factor binding protein 1 54823 SWT1 SWT1, RNA endoribonuclease homolog 9984 THOC1 THO complex 1 57187 THOC2 THO complex 2 84321 THOC3 THO complex 3 8563 THOC5 THO complex 5 79228 THOC6 THO complex 6 305714 THOC7 THO complex 7 3842 TNPO1 transportin 1 23534 TNPO3 transportin 3 79084 WDR77 WD repeat domain 77 64328 XPO4 exportin 4 79413 ZBED2 zinc finger BED-type containing 2 85437 ZCRB1 zinc finger CCHC-type and RNA binding motif containing 1 7756 ZNF207 zinc finger protein 207

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 5.56e-01 3.77e-17 GO THO complex part of transcription export complex cellular_component 1.19e-01 3.96e-03 Reactome NOSIP mediated eNOS trafficking Metabolism 9.92e-02 6.17e-19 GO transcription export complex cellular_component 7.51e-02 2.66e-09 Reactome SLBP independent Processing of Histone Pre-mRNAs Metabolism of RNA 7.37e-02 1.48e-14 Reactome snRNP Assembly Metabolism of RNA 7.28e-02 1.48e-14 Reactome Metabolism of non-coding RNA Metabolism of RNA 3.37e-02 5.91e-24 GO RNA export from nucleus biological_process 3.02e-02 1.54e-06 GO nuclear export biological_process 1.75e-02 1.86e-28 Reactome Cleavage of Growing Transcript in the Termination Region Gene expression (Transcription) 1.65e-02 1.86e-28 Reactome RNA Polymerase II Transcription Termination Gene expression (Transcription) 1.04e-02 1.19e-24 Reactome mRNA 3'-end processing Metabolism of RNA 2.61e-03 3.40e-23 Reactome Transport of Mature mRNA derived from an Intron-Containing Transcript Metabolism of RNA 6.74e-04 1.69e-04 GO primary miRNA processing biological_process 5.18e-04 1.54e-06 GO SMN complex 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 RNA splicing, via transesterification reactions 0e+00 0e+00 RNA splicing 0e+00 0e+00 mRNA metabolic process 0e+00 0e+00 mRNA processing 0e+00 0e+00 mRNA splicing, via spliceosome 0e+00 0e+00 RNA 3'-end processing 0e+00 0e+00 transcription from RNA polymerase II promoter 0e+00 0e+00 termination of RNA polymerase II transcription 0e+00 0e+00 RNA localization 0e+00 0e+00 nuclear transport 0e+00 0e+00 nucleocytoplasmic transport 0e+00 0e+00 nuclear export 0e+00 0e+00 RNA transport 0e+00 0e+00 mRNA transport 0e+00 0e+00 DNA-templated transcription, termination 0e+00 0e+00 protein export from nucleus 0e+00 0e+00 mRNA export from nucleus 0e+00 0e+00 RNA export from nucleus 0e+00 0e+00 ribonucleoprotein complex localization 0e+00 0e+00 mRNA 3'-end processing

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 METABOLISM OF NON CODING RNA 0.00e+00 0.00e+00 METABOLISM OF RNA 3.53e-11 1.01e-08 METABOLISM OF NON CODING RNA 1.68e-10 6.00e-08 CLEAVAGE OF GROWING TRANSCRIPT IN THE TERMINATION REGION 2.26e-09 5.29e-07 METABOLISM OF RNA 8.90e-09 2.63e-06 SLBP DEPENDENT PROCESSING OF REPLICATION DEPENDENT HISTONE PRE MRNAS 1.26e-08 3.65e-06 PROCESSING OF CAPPED INTRONLESS PRE MRNA 3.57e-08 7.36e-06 CLEAVAGE OF GROWING TRANSCRIPT IN THE TERMINATION REGION 1.30e-07 2.50e-05 SLBP DEPENDENT PROCESSING OF REPLICATION DEPENDENT HISTONE PRE MRNAS 2.15e-07 5.36e-05 RNA POL II TRANSCRIPTION 3.32e-07 8.00e-05 MRNA 3 END PROCESSING 6.67e-07 1.19e-04 PROCESSING OF CAPPED INTRONLESS PRE MRNA 8.50e-06 1.65e-03 MRNA PROCESSING 9.25e-06 1.38e-03 RNA POL II TRANSCRIPTION 1.56e-05 2.88e-03 MRNA SPLICING 1.79e-05 3.26e-03 TRANSCRIPTION 2.07e-05 3.73e-03 PROCESSING OF INTRONLESS PRE MRNAS 3.18e-05 4.40e-03 MRNA 3 END PROCESSING 4.70e-05 7.88e-03 MRNA SPLICING MINOR PATHWAY 9.06e-05 1.17e-02 MRNA SPLICING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.77e-05 6.96e-02 paraparesis 5.96e-05 1.60e-01 tail necrosis 7.50e-05 1.87e-01 complete embryonic lethality between implantation and somite formation 2.63e-04 4.13e-01 epidermal necrosis 4.25e-04 5.52e-01 hyperresponsive to tactile stimuli 4.31e-04 5.55e-01 hyperalgesia 4.85e-04 5.97e-01 abnormal endplate potential 6.65e-04 7.18e-01 increased skeletal muscle fiber size 7.88e-04 7.83e-01 enhanced coordination 8.78e-04 8.36e-01 abnormal miniature endplate potential 1.03e-03 9.16e-01 failure to form blastocele 1.38e-03 1.00e+00 failure of blastocyst to hatch from the zona pellucida 1.53e-03 1.00e+00 abnormal synaptic transmission 1.87e-03 1.00e+00 decreased skeletal muscle fiber size 2.74e-03 1.00e+00 decreased thermal nociceptive threshold 3.01e-03 1.00e+00 complete embryonic lethality before implantation 3.36e-03 1.00e+00 decreased motor neuron number 3.74e-03 1.00e+00 increased ovary weight 3.75e-03 1.00e+00 abnormal dermal mast cell morphology 4.11e-03 1.00e+00 distended pericardium

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

²FDR corrected p-value (Benjamini-Hochberg)