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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod28

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod28 Module size 59 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 284040 CDRT4 CMT1A duplicated region transcript 4 144717 FAM109A PH domain containing endocytic trafficking adaptor 1 9896 FIG4 FIG4 phosphoinositide 5-phosphatase 3612 IMPA1 inositol monophosphatase 1 3613 IMPA2 inositol monophosphatase 2 54928 IMPAD1 inositol monophosphatase domain containing 1 3628 INPP1 inositol polyphosphate-1-phosphatase 3631 INPP4A inositol polyphosphate-4-phosphatase type I A 8821 INPP4B inositol polyphosphate-4-phosphatase type II B 3632 INPP5A inositol polyphosphate-5-phosphatase A 56623 INPP5E inositol polyphosphate-5-phosphatase E 4952 INPP5F OCRL, inositol polyphosphate-5-phosphatase 27124 INPP5J inositol polyphosphate-5-phosphatase J 51763 INPP5K inositol polyphosphate-5-phosphatase K 9807 IP6K1 inositol hexakisphosphate kinase 1 253430 IPMK inositol polyphosphate multikinase 64768 IPPK inositol-pentakisphosphate 2-kinase 3705 ITPK1 inositol-tetrakisphosphate 1-kinase 3706 ITPKA inositol-trisphosphate 3-kinase A 3707 ITPKB inositol-trisphosphate 3-kinase B 80271 ITPKC inositol-trisphosphate 3-kinase C 3708 ITPR1 inositol 1,4,5-trisphosphate receptor type 1 3709 ITPR2 inositol 1,4,5-trisphosphate receptor type 2 3710 ITPR3 inositol 1,4,5-trisphosphate receptor type 3 9562 MINPP1 multiple inositol-polyphosphate phosphatase 1 4534 MTM1 myotubularin 1 8776 MTMR1 myotubularin related protein 1 54893 MTMR10 myotubularin related protein 10 10903 MTMR11 myotubularin related protein 11 64419 MTMR14 myotubularin related protein 14 8898 MTMR2 myotubularin related protein 2 8897 MTMR3 myotubularin related protein 3 9110 MTMR4 myotubularin related protein 4 9107 MTMR6 myotubularin related protein 6 9108 MTMR7 myotubularin related protein 7 55613 MTMR8 myotubularin related protein 8 66036 MTMR9 myotubularin related protein 9 5297 PI4KA phosphatidylinositol 4-kinase alpha 5286 PIK3C2A phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha 5287 PIK3C2B phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta 5288 PIK3C2G phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 gamma 5305 PIP4K2A phosphatidylinositol-5-phosphate 4-kinase type 2 alpha 8396 PIP4K2B phosphatidylinositol-5-phosphate 4-kinase type 2 beta 79837 PIP4K2C phosphatidylinositol-5-phosphate 4-kinase type 2 gamma 8394 PIP5K1A phosphatidylinositol-4-phosphate 5-kinase type 1 alpha 8395 PIP5K1B phosphatidylinositol-4-phosphate 5-kinase type 1 beta 23396 PIP5K1C phosphatidylinositol-4-phosphate 5-kinase type 1 gamma 138429 PIP5KL1 phosphatidylinositol-4-phosphate 5-kinase like 1 5333 PLCD1 phospholipase C delta 1 113026 PLCD3 phospholipase C delta 3 84812 PLCD4 phospholipase C delta 4 51196 PLCE1 phospholipase C epsilon 1 89869 PLCZ1 phospholipase C zeta 1 85477 SCIN scinderin 8867 SYNJ1 synaptojanin 1 8871 SYNJ2 synaptojanin 2 374882 TMEM205 transmembrane protein 205 29850 TRPM5 transient receptor potential cation channel subfamily M member 5 55697 VAC14 Vac14, PIKFYVE complex component

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 4.84e-01 3.20e-31 GO phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity molecular_function 4.49e-01 5.68e-15 GO 1-phosphatidylinositol-4-phosphate 5-kinase activity molecular_function 2.25e-01 3.20e-03 Reactome Synthesis of IPs in the ER lumen Metabolism 2.02e-01 4.51e-26 GO inositol phosphate dephosphorylation biological_process 1.88e-01 3.76e-22 Reactome Synthesis of PIPs at the early endosome membrane Metabolism 1.65e-01 2.18e-10 GO inositol phosphate-mediated signaling biological_process 1.52e-01 5.73e-47 Reactome Inositol phosphate metabolism Metabolism 1.46e-01 1.24e-07 Reactome Synthesis of PIPs in the nucleus Metabolism 1.33e-01 1.08e-06 GO 1-phosphatidylinositol-4-phosphate 3-kinase activity molecular_function 1.32e-01 1.24e-07 Reactome Synthesis of IPs in the nucleus Metabolism 1.09e-01 3.71e-13 GO inositol phosphate biosynthetic process biological_process 8.46e-02 6.06e-42 GO inositol phosphate metabolic process biological_process 8.18e-02 2.57e-06 GO platelet dense tubular network membrane cellular_component 7.86e-02 3.58e-59 GO phosphatidylinositol biosynthetic process biological_process 4.67e-02 9.62e-60 Reactome PI Metabolism Metabolism 4.66e-02 8.38e-32 GO phosphatidylinositol-3-phosphatase activity molecular_function 2.86e-02 3.67e-06 Reactome CLEC7A (Dectin-1) induces NFAT activation Immune System 2.05e-02 8.69e-06 GO inositol 1,4,5 trisphosphate binding molecular_function 3.34e-03 7.27e-23 GO phosphatidylinositol phosphorylation 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 0e+00 0e+00 phospholipid dephosphorylation 0e+00 0e+00 phosphatidylinositol biosynthetic process 0e+00 0e+00 phospholipid metabolic process 0e+00 0e+00 phosphatidylinositol dephosphorylation 0e+00 0e+00 glycerolipid metabolic process 0e+00 0e+00 dephosphorylation 0e+00 0e+00 lipid biosynthetic process 0e+00 0e+00 phospholipid biosynthetic process 0e+00 0e+00 phosphatidylinositol metabolic process 0e+00 0e+00 glycerophospholipid metabolic process 0e+00 0e+00 glycerophospholipid biosynthetic process 0e+00 0e+00 lipid modification 0e+00 0e+00 inositol phosphate metabolic process 0e+00 0e+00 phosphorylated carbohydrate dephosphorylation 0e+00 0e+00 phosphatidylinositol phosphorylation 0e+00 0e+00 alcohol metabolic process 0e+00 0e+00 inositol phosphate dephosphorylation 0e+00 0e+00 lipid phosphorylation 0e+00 0e+00 alcohol catabolic process 0e+00 0e+00 inositol phosphate catabolic process

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 PI METABOLISM 0.00e+00 0.00e+00 PHOSPHOLIPID METABOLISM 0.00e+00 0.00e+00 SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE 0.00e+00 0.00e+00 SYNTHESIS OF PIPS AT THE LATE ENDOSOME MEMBRANE 0.00e+00 0.00e+00 PI METABOLISM 0.00e+00 0.00e+00 PHOSPHOLIPID METABOLISM 0.00e+00 0.00e+00 SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE 0.00e+00 0.00e+00 SYNTHESIS OF PIPS AT THE LATE ENDOSOME MEMBRANE 0.00e+00 0.00e+00 SYNTHESIS OF PIPS AT THE EARLY ENDOSOME MEMBRANE 8.75e-12 3.38e-09 SYNTHESIS OF PIPS AT THE EARLY ENDOSOME MEMBRANE 1.54e-09 3.67e-07 SYNTHESIS OF PIPS AT THE GOLGI MEMBRANE 4.90e-09 1.48e-06 SYNTHESIS OF PIPS AT THE GOLGI MEMBRANE 8.38e-04 8.58e-02 ELEVATION OF CYTOSOLIC CA2 LEVELS 1.08e-03 1.26e-01 ELEVATION OF CYTOSOLIC CA2 LEVELS 2.78e-03 2.48e-01 PLATELET CALCIUM HOMEOSTASIS 3.97e-03 3.37e-01 EFFECTS OF PIP2 HYDROLYSIS 5.52e-03 4.44e-01 DAG AND IP3 SIGNALING 6.26e-03 4.97e-01 ANTIGEN ACTIVATES B CELL RECEPTOR LEADING TO GENERATION OF SECOND MESSENGERS 7.00e-03 6.00e-01 PLATELET CALCIUM HOMEOSTASIS 9.19e-03 7.48e-01 EFFECTS OF PIP2 HYDROLYSIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.05e-04 5.36e-01 abnormal gustatory system physiology 1.39e-03 1.00e+00 spongiform encephalopathy 1.50e-03 1.00e+00 abnormal involuntary movement 1.66e-03 1.00e+00 decreased fertilization frequency 1.75e-03 1.00e+00 increased synaptic depression 2.57e-03 1.00e+00 short humerus 2.70e-03 1.00e+00 short ulna 3.75e-03 1.00e+00 abnormal sciatic nerve morphology 5.06e-03 1.00e+00 decreased bone volume 5.45e-03 1.00e+00 abnormal locomotor coordination 5.62e-03 1.00e+00 abnormal sensory ganglion morphology 6.49e-03 1.00e+00 abnormal nerve conduction 7.48e-03 1.00e+00 absent thymus medulla 7.92e-03 1.00e+00 abnormal heart atrium morphology 7.98e-03 1.00e+00 ataxia 9.35e-03 1.00e+00 axial skeleton hypoplasia 9.47e-03 1.00e+00 increased response of heart to induced stress 1.12e-02 1.00e+00 small clavicle 1.12e-02 1.00e+00 aortic valve regurgitation 1.12e-02 1.00e+00 thick pulmonary valve

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

²FDR corrected p-value (Benjamini-Hochberg)