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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod316

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod316 Module size 50 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 84962 AJUBA ajuba LIM protein 10142 AKAP9 A-kinase anchoring protein 9 7840 ALMS1 ALMS1, centrosome and basal body associated protein 51582 AZI1 antizyme inhibitor 1 79866 BORA bora, aurora kinase A activator 9738 CCP110 centriolar coiled-coil protein 110 55755 CDK5RAP2 CDK5 regulatory subunit associated protein 2 55835 CENPJ centromere protein J 9662 CEP135 centrosomal protein 135 22995 CEP152 centrosomal protein 152 22897 CEP164 centrosomal protein 164 55125 CEP192 centrosomal protein 192 11190 CEP250 centrosomal protein 250 80184 CEP290 centrosomal protein 290 9702 CEP57 centrosomal protein 57 80254 CEP63 centrosomal protein 63 80321 CEP70 centrosomal protein 70 55722 CEP72 centrosomal protein 72 79959 CEP76 centrosomal protein 76 84131 CEP78 centrosomal protein 78 51266 CLEC1B C-type lectin domain family 1 member B 11064 CNTRL centriolin 11258 DCTN3 dynactin subunit 3 1781 DYNC1I2 dynein cytoplasmic 1 intermediate chain 2 11116 FGFR1OP FGFR1 oncogene partner 139378 GPR112 adhesion G protein-coupled receptor G4 55142 HAUS2 HAUS augmin like complex subunit 2 440145 MZT1 mitotic spindle organizing protein 1 653784 MZT2A mitotic spindle organizing protein 2A 80097 MZT2B mitotic spindle organizing protein 2B 121441 NEDD1 neural precursor cell expressed, developmentally down-regulated 1 4751 NEK2 NIMA related kinase 2 22981 NINL ninein like 338323 NLRP14 NLR family pyrin domain containing 14 4957 ODF2 outer dense fiber of sperm tails 2 8481 OFD1 OFD1, centriole and centriolar satellite protein 10133 OPTN optineurin 5108 PCM1 pericentriolar material 1 5116 PCNT pericentrin 10733 PLK4 polo like kinase 4 10806 SDCCAG8 serologically defined colon cancer antigen 8 9814 SFI1 SFI1 centrin binding protein 8636 SSNA1 SS nuclear autoantigen 1 27175 TUBG2 tubulin gamma 2 10844 TUBGCP2 tubulin gamma complex associated protein 2 10426 TUBGCP3 tubulin gamma complex associated protein 3 27229 TUBGCP4 tubulin gamma complex associated protein 4 114791 TUBGCP5 tubulin gamma complex associated protein 5 85378 TUBGCP6 tubulin gamma complex associated protein 6 219578 ZNF804B zinc finger protein 804B

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 2.62e-01 5.75e-18 GO gamma-tubulin ring complex cellular_component 1.57e-01 2.97e-98 Reactome Recruitment of NuMA to mitotic centrosomes Cell Cycle 1.12e-01 6.16e-98 Reactome Centrosome maturation Cell Cycle 1.09e-01 6.16e-98 Reactome Recruitment of mitotic centrosome proteins and complexes Cell Cycle 7.55e-02 1.09e-18 GO centriole replication biological_process 5.48e-02 4.34e-20 GO gamma-tubulin binding molecular_function 5.45e-02 1.38e-13 GO microtubule minus-end binding molecular_function 3.66e-02 8.30e-77 Reactome Regulation of PLK1 Activity at G2/M Transition Cell Cycle 1.72e-02 8.81e-35 GO centriole cellular_component 7.84e-03 5.23e-17 GO mitotic spindle assembly biological_process 7.09e-03 1.14e-11 GO pericentriolar material cellular_component 4.00e-03 3.99e-89 Reactome G2/M Transition Cell Cycle 9.99e-04 7.01e-89 Reactome Mitotic G2-G2/M phases Cell Cycle

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 spindle organization 0e+00 0e+00 organelle assembly 0e+00 0e+00 centrosome cycle 0e+00 0e+00 mitotic cell cycle process 0e+00 0e+00 mitotic cell cycle 0e+00 0e+00 microtubule-based process 0e+00 0e+00 spindle assembly 0e+00 0e+00 microtubule nucleation 0e+00 0e+00 mitotic nuclear division 0e+00 0e+00 microtubule polymerization 0e+00 0e+00 microtubule cytoskeleton organization 0e+00 0e+00 microtubule polymerization or depolymerization 0e+00 0e+00 centrosome organization 0e+00 0e+00 centrosome duplication 0e+00 0e+00 microtubule organizing center organization 0e+00 0e+00 cilium assembly 0e+00 0e+00 membrane docking 0e+00 0e+00 cell cycle G2/M phase transition 0e+00 0e+00 cell projection assembly 0e+00 0e+00 mitotic cell cycle phase transition

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 CELL CYCLE 0.00e+00 0.00e+00 RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES 0.00e+00 0.00e+00 MITOTIC G2 G2 M PHASES 0.00e+00 0.00e+00 CELL CYCLE MITOTIC 0.00e+00 0.00e+00 LOSS OF NLP FROM MITOTIC CENTROSOMES 0.00e+00 0.00e+00 RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES 0.00e+00 0.00e+00 MITOTIC G2 G2 M PHASES 0.00e+00 0.00e+00 LOSS OF NLP FROM MITOTIC CENTROSOMES 1.50e-09 3.58e-07 RECRUITMENT OF NUMA TO MITOTIC CENTROSOMES 1.14e-08 3.32e-06 RECRUITMENT OF NUMA TO MITOTIC CENTROSOMES 1.04e-03 1.22e-01 SIGNALING BY FGFR1 FUSION MUTANTS 1.07e-03 1.25e-01 SIGNALING BY FGFR1 MUTANTS 1.24e-03 1.41e-01 SIGNALING BY FGFR MUTANTS 1.82e-03 1.71e-01 SIGNALING BY FGFR1 FUSION MUTANTS 2.36e-03 2.46e-01 SIGNALING BY FGFR IN DISEASE 3.17e-03 2.79e-01 SIGNALING BY FGFR1 MUTANTS 5.37e-03 4.36e-01 SIGNALING BY FGFR MUTANTS 1.03e-02 8.15e-01 CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII 1.37e-02 1.00e+00 RAS ACTIVATION UOPN CA2 INFUX THROUGH NMDA RECEPTOR 1.71e-02 1.00e+00 CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF RAS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.09e-04 2.40e-01 photoreceptor inner segment degeneration 1.17e-04 2.50e-01 polycystic kidney 1.50e-04 2.95e-01 abnormal mitosis 5.49e-04 6.42e-01 abnormal mitotic spindle morphology 6.59e-04 7.15e-01 photoreceptor outer segment degeneration 6.92e-04 7.31e-01 kidney cysts 9.26e-04 8.63e-01 renal glomerulus cysts 2.29e-03 1.00e+00 abnormal retinal photoreceptor morphology 2.52e-03 1.00e+00 abnormal parietal bone morphology 5.52e-03 1.00e+00 enlarged kidney 5.62e-03 1.00e+00 iris synechia 5.64e-03 1.00e+00 small sacral vertebrae 6.44e-03 1.00e+00 retinal photoreceptor degeneration 7.25e-03 1.00e+00 abnormal head morphology 7.40e-03 1.00e+00 atrial septal defect 9.35e-03 1.00e+00 inlet ventricular septal defect 9.38e-03 1.00e+00 short lumbar vertebrae 1.12e-02 1.00e+00 decreased lymphatic vessel endothelial cell number 1.12e-02 1.00e+00 abnormal Descemet membrane 1.12e-02 1.00e+00 abnormal external male genitalia morphology

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

²FDR corrected p-value (Benjamini-Hochberg)