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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod235

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod235 Module size 64 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 55109 AGGF1 angiogenic factor with G-patch and FHA domains 1 221120 ALKBH3 alkB homolog 3, alpha-ketoglutaratedependent dioxygenase 27350 APOBEC3C apolipoprotein B mRNA editing enzyme catalytic subunit 3C 55082 ARGLU1 arginine and glutamate rich 1 51329 ARL6IP4 ADP ribosylation factor like GTPase 6 interacting protein 4 79969 ATAT1 alpha tubulin acetyltransferase 1 9774 BCLAF1 BCL2 associated transcription factor 1 79864 C11orf63 junctional cadherin complex regulator 56905 C15orf39 chromosome 15 open reading frame 39 123970 C16orf78 chromosome 16 open reading frame 78 57035 C1orf63 arginine and serine rich protein 1 404220 C6orf201 chromosome 6 open reading frame 201 58509 CACTIN cactin, spliceosome C complex subunit 10523 CHERP calcium homeostasis endoplasmic reticulum protein 10229 CLK1 coenzyme Q7, hydroxylase 1196 CLK2 CDC like kinase 2 1198 CLK3 CDC like kinase 3 158511 CSAG1 chondrosarcoma associated gene 1 63932 CXorf56 chromosome X open reading frame 56 11083 DIO1 death inducer-obliterator 1 64097 EPB41L4A erythrocyte membrane protein band 4.1 like 4A 221786 FAM200A family with sequence similarity 200 member A 118924 FRA10AC1 FRA10A associated CGG repeat 1 94104 GCFC1 PAX3 and PAX7 binding protein 1 221188 GPR114 adhesion G protein-coupled receptor G5 9324 HMGN3 high mobility group nucleosomal binding domain 3 3550 IK IK cytokine 84542 KIAA1841 KIAA1841 84648 LCE3D late cornified envelope 3D 221091 LRRN4CL LRRN4 C-terminal like 126868 MAB21L3 mab-21 like 3 4795 NFKBIL1 NFKB inhibitor like 1 79576 NKAP NFKB activating protein 84081 NSRP1 nuclear speckle splicing regulatory protein 1 56122 PCDHB14 protocadherin beta 14 25957 PNISR PNN interacting serine and arginine rich protein 5411 PNN pinin, desmosome associated protein 5546 PRCC proline rich mitotic checkpoint control factor 84950 PRPF38A pre-mRNA processing factor 38A 55119 PRPF38B pre-mRNA processing factor 38B 84991 RBM17 RNA binding motif protein 17 55147 RBM23 RNA binding motif protein 23 9584 RBM39 RNA binding motif protein 39 10179 RBM7 RNA binding motif protein 7 5940 RBMY1A1 RNA binding motif protein, Y-linked, family 1, member A1 159163 RBMY1F RNA binding motif protein, Y-linked, family 1, member F 140730 RIMS4 regulating synaptic membrane exocytosis 4 8293 SERF1A small EDRK-rich factor 1A 11017 SNRNP27 small nuclear ribonucleoprotein U4/U6.U5 subunit 27 10407 SPAG11B sperm associated antigen 11B 441525 SPANXN4 SPANX family member N4 6732 SRPK1 SRSF protein kinase 1 6733 SRPK2 SRSF protein kinase 2 83551 TAAR8 trace amine associated receptor 8 55145 THAP1 THAP domain containing 1 114034 TOE1 target of EGR1, exonuclease 29896 TRA2A transformer 2 alpha homolog 151613 TTC14 tetratricopeptide repeat domain 14 23350 U2SURP U2 snRNP associated SURP domain containing 58486 ZBED5 zinc finger BED-type containing 5 54819 ZCCHC10 zinc finger CCHC-type containing 10 91603 ZNF830 zinc finger protein 830 7310 ZRSR1 ZRSR2 pseudogene 1 8233 ZRSR2 zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2

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 7.61e-02 1.34e-04 GO U2AF cellular_component 2.78e-02 7.67e-03 Reactome Regulation of thyroid hormone activity Metabolism 2.39e-02 1.12e-06 GO regulation of RNA splicing biological_process 2.07e-02 3.48e-04 GO negative regulation of lipopolysaccharide-mediated signaling pathway biological_process 1.42e-02 7.01e-12 GO RNA splicing biological_process 8.06e-03 4.16e-04 GO regulation of mRNA processing biological_process 1.88e-03 3.47e-05 GO spliceosomal complex assembly biological_process 1.66e-03 5.07e-07 GO regulation of alternative mRNA splicing, via spliceosome biological_process 9.65e-04 5.47e-05 GO protein serine/threonine/tyrosine kinase activity molecular_function

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 0.00e+00 0.00e+00 mRNA metabolic process 0.00e+00 0.00e+00 mRNA processing 0.00e+00 0.00e+00 nuclear speck 1.81e-11 1.61e-08 mRNA splicing, via spliceosome 3.22e-11 2.80e-08 RNA splicing, via transesterification reactions 4.56e-10 3.53e-07 regulation of RNA splicing 5.27e-10 2.46e-07 nuclear body 3.13e-08 1.16e-05 spliceosomal complex 1.37e-06 6.35e-04 regulation of mRNA splicing, via spliceosome 8.42e-06 3.32e-03 regulation of mRNA processing 2.30e-05 5.60e-03 protein serine/threonine/tyrosine kinase activity 4.06e-05 1.34e-02 negative regulation of viral genome replication 5.37e-05 1.13e-02 U2AF 5.82e-05 1.83e-02 negative regulation of lipopolysaccharide-mediated signaling pathway 7.59e-05 1.54e-02 precatalytic spliceosome 8.17e-05 1.65e-02 intracellular ribonucleoprotein complex 8.27e-05 1.67e-02 ribonucleoprotein complex 1.24e-04 3.51e-02 regulation of alternative mRNA splicing, via spliceosome 1.37e-04 2.71e-02 protein serine/threonine kinase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 6.64e-03 5.76e-01 AMINE DERIVED HORMONES 2.20e-02 1.00e+00 AMINE DERIVED HORMONES 2.93e-02 1.00e+00 AMINE LIGAND BINDING RECEPTORS 3.00e-02 1.00e+00 AMINE LIGAND BINDING RECEPTORS 3.75e-02 1.00e+00 DNA REPAIR

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.79e-03 1e+00 increased grip strength 1.87e-03 1e+00 increased thyroxine level 1.87e-03 1e+00 embryonic lethality prior to tooth bud stage 1.91e-03 1e+00 abnormal midbrain-hindbrain boundary morphology 3.74e-03 1e+00 abnormal mesenchymal cell differentiation involved in lung development 3.76e-03 1e+00 decreased hair follicle number 5.61e-03 1e+00 increased triiodothyronine level 5.62e-03 1e+00 thick lung-associated mesenchyme 7.47e-03 1e+00 abnormal thyroid hormone level 7.47e-03 1e+00 absent trophectoderm cell proliferation 7.51e-03 1e+00 abnormal thyroid physiology 9.34e-03 1e+00 increased circulating thyroxine level 9.34e-03 1e+00 increased circulating triiodothyronine level 1.14e-02 1e+00 abnormal retina morphology 1.30e-02 1e+00 abnormal sperm annulus morphology 1.31e-02 1e+00 thin dermal layer 1.31e-02 1e+00 transposition of great arteries 1.39e-02 1e+00 increased body weight 1.49e-02 1e+00 short sperm flagellum 1.49e-02 1e+00 decreased epididymis weight

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

²FDR corrected p-value (Benjamini-Hochberg)