Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod325

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod325 Module size 46 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 810 CALML3 calmodulin like 3 51806 CALML5 calmodulin like 5 163688 CALML6 calmodulin like 6 79012 CAMKV CaM kinase like vesicle associated 828 CAPS calcyphosine 84698 CAPS2 calcyphosine 2 133690 CAPSL calcyphosine like 8556 CDC14A cell division cycle 14A 195828 CDC14B zinc finger protein 367 289993 CDKN3 cyclin-dependent kinase inhibitor 3 1069 CETN2 centrin 2 26973 CHP1 cysteine and histidine rich domain containing 1 63928 CHP2 calcineurin like EF-hand protein 2 10519 CIB1 calcium and integrin binding 1 130106 CIB4 calcium and integrin binding family member 4 1612 DAPK1 death associated protein kinase 1 114971 DUSP23 protein tyrosine phosphatase, mitochondrial 1 1859 DYRK1A dual specificity tyrosine phosphorylation regulated kinase 1A 9149 DYRK1B dual specificity tyrosine phosphorylation regulated kinase 1B 8445 DYRK2 dual specificity tyrosine phosphorylation regulated kinase 2 8444 DYRK3 dual specificity tyrosine phosphorylation regulated kinase 3 8798 DYRK4 dual specificity tyrosine phosphorylation regulated kinase 4 204851 HIPK1 homeodomain interacting protein kinase 1 28996 HIPK2 homeodomain interacting protein kinase 2 10114 HIPK3 homeodomain interacting protein kinase 3 147746 HIPK4 homeodomain interacting protein kinase 4 9833 MELK maternal embryonic leucine zipper kinase 85366 MYLK2 myosin light chain kinase 2 91807 MYLK3 myosin light chain kinase 3 10908 PNPLA6 patatin like phospholipase domain containing 6 5475 PPEF1 protein phosphatase with EF-hand domain 1 5470 PPEF2 protein phosphatase with EF-hand domain 2 5532 PPP3CB protein phosphatase 3 catalytic subunit beta 5533 PPP3CC protein phosphatase 3 catalytic subunit gamma 5534 PPP3R1 protein phosphatase 3 regulatory subunit B, alpha 5535 PPP3R2 protein phosphatase 3 regulatory subunit B, beta 5531 PPP4C protein phosphatase 4 catalytic subunit 5536 PPP5C protein phosphatase 5 catalytic subunit 100506012 PPP5D1 PPP5 tetratricopeptide repeat domain containing 1 138639 PTPDC1 protein tyrosine phosphatase domain containing 1 10290 SPEG SPEG complex locus 54997 TESC tescalcin 100287898 TTC34 tetratricopeptide repeat domain 34 127933 UHMK1 U2AF homology motif kinase 1 54503 ZDHHC13 zinc finger DHHC-type containing 13 339500 ZNF678 zinc finger protein 678

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 3.16e-01 1.26e-07 GO calcineurin complex cellular_component 2.00e-01 3.33e-05 GO myosin light chain kinase activity molecular_function 6.82e-02 6.85e-09 GO protein serine/threonine/tyrosine kinase activity molecular_function 5.78e-02 2.12e-14 GO protein serine/threonine phosphatase activity molecular_function 4.26e-02 2.39e-07 GO calmodulin-dependent protein kinase activity molecular_function 2.68e-02 4.24e-08 GO protein tyrosine/serine/threonine phosphatase activity molecular_function 1.56e-02 2.47e-05 GO enzyme regulator activity molecular_function 1.29e-02 3.61e-04 GO embryonic camera-type eye morphogenesis biological_process 3.24e-03 3.97e-05 GO intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator biological_process 1.88e-03 4.26e-04 GO negative regulation of calcineurin-NFAT signaling cascade 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 dephosphorylation 0.00e+00 0.00e+00 protein dephosphorylation 0.00e+00 0.00e+00 calcium ion binding 0.00e+00 0.00e+00 protein kinase activity 0.00e+00 0.00e+00 protein serine/threonine kinase activity 0.00e+00 0.00e+00 protein serine/threonine phosphatase activity 0.00e+00 0.00e+00 phosphoprotein phosphatase activity 5.29e-10 2.93e-07 phosphotransferase activity, alcohol group as acceptor 5.88e-10 3.22e-07 phosphatase activity 1.77e-08 7.77e-06 phosphoric ester hydrolase activity 4.06e-08 2.43e-05 peptidyl-serine phosphorylation 5.79e-08 3.39e-05 peptidyl-threonine phosphorylation 7.13e-07 2.32e-04 protein serine/threonine/tyrosine kinase activity 2.86e-06 8.30e-04 protein tyrosine/serine/threonine phosphatase activity 3.40e-06 9.74e-04 hydrolase activity, acting on ester bonds 9.30e-06 2.44e-03 calmodulin-dependent protein kinase activity 1.17e-05 4.46e-03 peptidyl-tyrosine dephosphorylation 2.09e-05 7.46e-03 regulation of signal transduction by p53 class mediator 2.49e-05 8.71e-03 regulation of calcineurin-NFAT signaling cascade 3.23e-05 7.15e-03 calcineurin complex

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.15e-04 1.44e-02 DARPP 32 EVENTS 1.77e-04 2.12e-02 OPIOID SIGNALLING 2.78e-03 2.48e-01 CONVERSION FROM APC C CDC20 TO APC C CDH1 IN LATE ANAPHASE 5.13e-03 4.20e-01 APOPTOSIS 5.25e-03 4.76e-01 DARPP 32 EVENTS 9.13e-03 6.81e-01 REGULATION OF MITOTIC CELL CYCLE 1.03e-02 7.50e-01 ACTIVATION OF BH3 ONLY PROTEINS 1.03e-02 7.50e-01 ROLE OF DCC IN REGULATING APOPTOSIS 1.20e-02 8.53e-01 REGULATION OF APOPTOSIS 2.36e-02 1.00e+00 G0 AND EARLY G1 3.37e-02 1.00e+00 INTRINSIC PATHWAY FOR APOPTOSIS 3.69e-02 1.00e+00 ROLE OF DCC IN REGULATING APOPTOSIS 4.64e-02 1.00e+00 LOSS OF NLP FROM MITOTIC CENTROSOMES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.09e-04 3.58e-01 decreased cellular sensitivity to ultraviolet irradiation 1.42e-03 1.00e+00 abnormal thalamus morphology 3.39e-03 1.00e+00 decreased neuron apoptosis 6.43e-03 1.00e+00 decreased brain weight 9.33e-03 1.00e+00 cardiac muscle necrosis 9.35e-03 1.00e+00 increased skeletal muscle fiber number 1.12e-02 1.00e+00 delayed chorioallantoic fusion 1.31e-02 1.00e+00 abnormal globus pallidus morphology 1.31e-02 1.00e+00 decreased superior colliculus size 1.50e-02 1.00e+00 abnormal Kupffer cell morphology 1.52e-02 1.00e+00 decreased cardiac muscle contractility 1.67e-02 1.00e+00 decreased pancreatic beta cell proliferation 1.68e-02 1.00e+00 decreased hindbrain size 1.68e-02 1.00e+00 increased placenta apoptosis 1.86e-02 1.00e+00 abnormal heart left ventricle pressure 2.04e-02 1.00e+00 abnormal brain size 2.04e-02 1.00e+00 decreased thoracic vertebrae number 2.04e-02 1.00e+00 decreased renal tubule apoptosis 2.04e-02 1.00e+00 reduced NMDA-mediated synaptic currents 2.05e-02 1.00e+00 abnormal synaptic bouton morphology

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

²FDR corrected p-value (Benjamini-Hochberg)