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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod17

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod17 Module size 66 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10121 ACTR1A ARP1 actin related protein 1 homolog A 158798 AKAP14 A-kinase anchoring protein 14 55156 ARMC1 armadillo repeat containing 1 79798 ARMC5 armadillo repeat containing 5 6790 AURKA aurora kinase A 54998 AURKAIP1 aurora kinase A interacting protein 1 84934 C12orf52 RBPJ interacting and tubulin associated 1 79780 CCDC82 coiled-coil domain containing 82 80212 CCDC92 coiled-coil domain containing 92 983 CDK1 cyclin dependent kinase 1 9857 CEP350 centrosomal protein 350 64793 CEP85 centrosomal protein 85 84902 CEP89 centrosomal protein 89 23332 CLASP1 cytoplasmic linker associated protein 1 9976 CLEC2B C-type lectin domain family 2 member B 170482 CLEC4C C-type lectin domain family 4 member C 1267 CNP 2',3'-cyclic nucleotide 3' phosphodiesterase 132864 CPEB2 cytoplasmic polyadenylation element binding protein 2 1453 CSNK1D casein kinase 1 delta 1454 CSNK1E casein kinase 1 epsilon 55861 DBNDD2 dysbindin domain containing 2 85458 DIXDC1 DIX domain containing 1 642273 FAM110C family with sequence similarity 110 member C 150864 FAM117B family with sequence similarity 117 member B 56181 FAM54B mitochondrial fission regulator 1 like 222584 FAM83B family with sequence similarity 83 member B 55138 FAM90A1 family with sequence similarity 90 member A1 115106 HAUS1 HAUS augmin like complex subunit 1 79441 HAUS3 HAUS augmin like complex subunit 3 54930 HAUS4 HAUS augmin like complex subunit 4 23354 HAUS5 HAUS augmin like complex subunit 5 54801 HAUS6 HAUS augmin like complex subunit 6 55559 HAUS7 HAUS augmin like complex subunit 7 93323 HAUS8 HAUS augmin like complex subunit 8 151050 KANSL1L KAT8 regulatory NSL complex subunit 1 like 3902 LAG3 lymphocyte activating 3 3957 LGALS2 galectin 2 79782 LRRC31 leucine rich repeat containing 31 149499 LRRC71 leucine rich repeat containing 71 89876 MAATS1 MYCBP associated and testis expressed 1 22919 MAPRE1 microtubule associated protein RP/EB family member 1 89796 NAV1 neuron navigator 1 79858 NEK11 NIMA related kinase 11 338321 NLRP9 NLR family pyrin domain containing 9 4926 NUMA1 nuclear mitotic apparatus protein 1 64430 PCNXL4 pecanex 4 5347 PLK1 polo like kinase 1 5577 PRKAR2B protein kinase cAMP-dependent type II regulatory subunit beta 55209 SETD5 SET domain containing 5 79856 SNX22 sorting nexin 22 28966 SNX24 sorting nexin 24 83891 SNX25 sorting nexin 25 64847 SPATA20 spermatogenesis associated 20 202051 SPATA24 spermatogenesis associated 24 375686 SPATC1 spermatogenesis and centriole associated 1 441273 SPDYE2 speedy/RINGO cell cycle regulator family member E2 56977 STOX2 storkhead box 2 6867 TACC1 transforming acidic coiled-coil containing protein 1 23424 TDRD7 tudor domain containing 7 59353 TMEM35 transmembrane protein 35A 199223 TTC21A tetratricopeptide repeat domain 21A 7846 TUBA1A tubulin alpha 1a 7277 TUBA4A tubulin alpha 4a 10382 TUBB4A tubulin beta 4A class IVa 10383 TUBB4B tubulin beta 4B class IVb 7283 TUBG1 tubulin gamma 1

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 4.18e-01 5.49e-17 GO HAUS complex cellular_component 9.60e-02 8.19e-38 Reactome AURKA Activation by TPX2 Cell Cycle 5.52e-02 6.05e-03 Reactome Interaction between PHLDA1 and AURKA Cell Cycle 4.19e-02 1.34e-04 Reactome Phosphorylation of Emi1 Cell Cycle 3.48e-02 1.06e-36 Reactome Recruitment of NuMA to mitotic centrosomes Cell Cycle 3.18e-02 4.30e-07 Reactome Post-chaperonin tubulin folding pathway Metabolism of proteins 2.03e-02 2.49e-04 GO cAMP-dependent protein kinase complex cellular_component 1.70e-02 1.06e-36 GO regulation of G2/M transition of mitotic cell cycle biological_process 1.60e-02 1.24e-06 GO microtubule bundle formation biological_process 1.38e-02 3.70e-09 GO spindle microtubule cellular_component 9.57e-03 1.87e-04 Reactome Activation of NIMA Kinases NEK9, NEK6, NEK7 Cell Cycle 8.40e-03 7.83e-36 Reactome Regulation of PLK1 Activity at G2/M Transition Cell Cycle 7.74e-03 1.74e-11 GO microtubule cytoskeleton organization biological_process 5.67e-03 5.24e-14 GO spindle cellular_component 5.47e-03 6.23e-35 GO ciliary basal body-plasma membrane docking biological_process 4.62e-03 1.24e-06 Reactome Prefoldin mediated transfer of substrate to CCT/TriC Metabolism of proteins 4.17e-03 6.58e-36 Reactome Loss of Nlp from mitotic centrosomes Cell Cycle 3.13e-03 1.43e-05 GO microtubule plus-end binding molecular_function 2.40e-03 6.58e-36 Reactome Loss of proteins required for interphase microtubule organization from the centrosome Cell Cycle 3.19e-04 7.96e-35 Reactome Anchoring of the basal body to the plasma membrane Organelle biogenesis and maintenance

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 mitotic cell cycle process 0e+00 0e+00 mitotic cell cycle phase transition 0e+00 0e+00 mitotic cell cycle 0e+00 0e+00 cell cycle phase transition 0e+00 0e+00 organelle 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 microtubule-based process 0e+00 0e+00 G2/M transition of mitotic cell cycle 0e+00 0e+00 cilium organization 0e+00 0e+00 cilium assembly 0e+00 0e+00 ciliary basal body docking 0e+00 0e+00 spindle organization 0e+00 0e+00 microtubule cytoskeleton organization 0e+00 0e+00 cell division 0e+00 0e+00 spindle assembly 0e+00 0e+00 centrosome organization 0e+00 0e+00 microtubule organizing center organization 0e+00 0e+00 microtubule

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 1.81e-07 4.54e-05 FORMATION OF TUBULIN FOLDING INTERMEDIATES BY CCT TRIC 2.28e-07 5.64e-05 POST CHAPERONIN TUBULIN FOLDING PATHWAY 3.26e-07 7.87e-05 PREFOLDIN MEDIATED TRANSFER OF SUBSTRATE TO CCT TRIC 6.99e-07 1.61e-04 RECRUITMENT OF NUMA TO MITOTIC CENTROSOMES 1.53e-06 2.58e-04 RECRUITMENT OF NUMA TO MITOTIC CENTROSOMES 1.56e-06 3.41e-04 PROTEIN FOLDING 1.81e-06 3.03e-04 POST CHAPERONIN TUBULIN FOLDING PATHWAY 8.55e-06 1.29e-03 FORMATION OF TUBULIN FOLDING INTERMEDIATES BY CCT TRIC 1.06e-05 1.57e-03 PREFOLDIN MEDIATED TRANSFER OF SUBSTRATE TO CCT TRIC 3.20e-05 4.42e-03 PROTEIN FOLDING 1.78e-03 1.68e-01 CYCLIN A B1 ASSOCIATED EVENTS DURING G2 M TRANSITION 2.00e-03 1.86e-01 PHOSPHORYLATION OF THE APC C

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 7.04e-06 3.67e-02 abnormal mitotic spindle morphology 5.19e-05 1.46e-01 prolonged circadian period 2.24e-04 3.74e-01 complete embryonic lethality before implantation 9.62e-04 8.85e-01 increased squamous cell carcinoma incidence 2.40e-03 1.00e+00 increased lung carcinoma incidence 2.98e-03 1.00e+00 abnormal cell nucleus morphology 3.75e-03 1.00e+00 increased CD8-positive, alpha-beta T cell number 5.63e-03 1.00e+00 increased single-positive T cell number 7.46e-03 1.00e+00 increased CD4-positive, alpha beta T cell number 7.47e-03 1.00e+00 decreased cervical vertebrae number 7.48e-03 1.00e+00 ocular hypertension 8.33e-03 1.00e+00 aneuploidy 8.81e-03 1.00e+00 embryonic growth arrest 9.33e-03 1.00e+00 enhanced humoral immune response 9.33e-03 1.00e+00 abnormal visual cortex morphology 9.36e-03 1.00e+00 hyperactivity 9.37e-03 1.00e+00 enlarged eye anterior chamber 1.12e-02 1.00e+00 increased mitotic index 1.12e-02 1.00e+00 abnormal cell nucleus count 1.12e-02 1.00e+00 decreased hippocampus pyramidal cell number

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

²FDR corrected p-value (Benjamini-Hochberg)