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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod294

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod294 Module size 27 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 112268437 AAK1 uncharacterized protein FLJ45252 55589 BMP2K BMP2 inducible kinase 54108 CHRAC1 chromatin accessibility complex subunit 1 23002 DAAM1 dishevelled associated activator of morphogenesis 1 23500 DAAM2 dishevelled associated activator of morphogenesis 2 414301 DDI1 DNA damage inducible 1 homolog 1 84301 DDI2 DNA damage inducible 1 homolog 2 2820 GPD2 glycerol-3-phosphate dehydrogenase 2 3850 KRT3 keratin 3 51350 KRT76 keratin 76 23175 LPIN1 lipin 1 9663 LPIN2 lipin 2 64900 LPIN3 lipin 3 360505 NPR3 NPR3-like, GATOR1 complex subunit 83714 NRIP2 nuclear receptor interacting protein 2 56675 NRIP3 nuclear receptor interacting protein 3 55361 PI4K2A phosphatidylinositol 4-kinase type 2 alpha 55300 PI4K2B phosphatidylinositol 4-kinase type 2 beta 5306 PITPNA phosphatidylinositol transfer protein alpha 23760 PITPNB phosphatidylinositol transfer protein beta 26207 PITPNC1 phosphatidylinositol transfer protein cytoplasmic 1 9600 PITPNM1 phosphatidylinositol transfer protein membrane associated 1 57605 PITPNM2 phosphatidylinositol transfer protein membrane associated 2 83394 PITPNM3 PITPNM family member 3 375775 PNPLA7 patatin like phospholipase domain containing 7 387893 SETD8 lysine methyltransferase 5A 7227 TRPS1 transcriptional repressor GATA binding 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 4.05e-01 1.81e-16 GO phosphatidylinositol transporter activity molecular_function 1.57e-01 2.95e-13 GO phosphatidylcholine transporter activity molecular_function 1.08e-01 3.29e-05 GO 1-phosphatidylinositol 4-kinase activity molecular_function 5.47e-02 3.07e-08 Reactome Synthesis of PI Metabolism 5.38e-02 4.29e-08 GO aspartic-type endopeptidase activity molecular_function 4.64e-02 8.72e-07 GO phosphatidate phosphatase activity molecular_function 4.64e-02 8.72e-07 Reactome Synthesis of PE Metabolism 3.65e-02 1.11e-06 GO fatty acid catabolic process biological_process 3.65e-02 1.11e-06 Reactome Triglyceride biosynthesis Metabolism 2.84e-02 1.38e-06 Reactome Depolymerisation of the Nuclear Lamina 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 4.33e-12 2.93e-09 phosphatidylinositol transporter activity 7.49e-11 6.30e-08 phospholipid transport 4.00e-10 3.12e-07 glycerophospholipid biosynthetic process 2.17e-09 1.55e-06 phospholipid biosynthetic process 6.30e-09 4.20e-06 glycerophospholipid metabolic process 2.40e-08 1.49e-05 glycerolipid metabolic process 3.05e-08 1.86e-05 phospholipid metabolic process 2.23e-07 1.19e-04 lipid transport 2.90e-07 1.02e-04 phospholipid transporter activity 3.90e-07 2.00e-04 lipid localization 3.92e-07 1.35e-04 phosphatidate phosphatase activity 6.84e-07 3.36e-04 lipid biosynthetic process 8.79e-07 4.22e-04 phosphatidylinositol biosynthetic process 1.34e-06 4.16e-04 aspartic-type endopeptidase activity 1.65e-06 5.04e-04 aspartic-type peptidase activity 2.21e-06 9.82e-04 phosphatidylethanolamine biosynthetic process 3.94e-06 1.67e-03 phosphatidylinositol metabolic process 5.65e-06 1.55e-03 lipid transporter activity 1.61e-05 5.93e-03 triglyceride biosynthetic process 2.53e-05 8.83e-03 organic anion transport

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.56e-06 3.41e-04 PHOSPHOLIPID METABOLISM 2.33e-06 3.82e-04 PHOSPHOLIPID METABOLISM 3.09e-06 4.98e-04 SYNTHESIS OF PE 3.47e-06 7.14e-04 SYNTHESIS OF PE 1.09e-05 2.08e-03 SYNTHESIS OF PC 1.93e-05 3.50e-03 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 5.92e-05 7.85e-03 SYNTHESIS OF PC 6.32e-05 8.35e-03 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 8.79e-05 1.13e-02 PI METABOLISM 1.33e-04 2.00e-02 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 1.62e-04 2.39e-02 PI METABOLISM 1.66e-04 2.44e-02 TRIGLYCERIDE BIOSYNTHESIS 3.27e-04 3.71e-02 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 5.27e-04 5.70e-02 TRIGLYCERIDE BIOSYNTHESIS 6.73e-04 8.33e-02 SYNTHESIS OF PIPS AT THE EARLY ENDOSOME MEMBRANE 6.77e-04 8.37e-02 SYNTHESIS OF PIPS AT THE GOLGI MEMBRANE 1.14e-03 1.13e-01 SYNTHESIS OF PIPS AT THE EARLY ENDOSOME MEMBRANE 1.22e-03 1.20e-01 SYNTHESIS OF PIPS AT THE GOLGI MEMBRANE 1.30e-03 1.27e-01 SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE 1.74e-03 1.89e-01 SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.88e-04 6.67e-01 decreased brown fat cell lipid droplet size 1.17e-03 9.85e-01 small thoracic cage 1.39e-03 1.00e+00 tremors 1.64e-03 1.00e+00 increased circulating alkaline phosphatase level 1.82e-03 1.00e+00 abnormal abdominal fat pad morphology 2.89e-03 1.00e+00 abnormal thoracic cage morphology 3.74e-03 1.00e+00 abnormal triiodothyronine level 3.92e-03 1.00e+00 decreased circulating LDL cholesterol level 4.99e-03 1.00e+00 decreased epididymal fat pad weight 5.61e-03 1.00e+00 abnormal vitamin absorption 7.80e-03 1.00e+00 decreased brown adipose tissue amount 8.00e-03 1.00e+00 delayed endochondral bone ossification 9.13e-03 1.00e+00 increased circulating aspartate transaminase level 9.35e-03 1.00e+00 decreased parametrial fat pad weight 9.35e-03 1.00e+00 decreased triglyceride lipase activity 1.08e-02 1.00e+00 demyelination 1.12e-02 1.00e+00 abnormal PNS glial cell morphology 1.12e-02 1.00e+00 decreased lipoprotein lipase activity 1.12e-02 1.00e+00 abnormal vitamin E level 1.12e-02 1.00e+00 decreased glycogen catabolism rate

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

²FDR corrected p-value (Benjamini-Hochberg)