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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod157

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod157 Module size 61 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 43 ACHE acetylcholinesterase (Cartwright blood group) 64850 AGXT2L1 ethanolamine-phosphate phospho-lyase 10079 ATP9A ATPase phospholipid transporting 9A (putative) 374868 ATP9B ATPase phospholipid transporting 9B (putative) 54978 C2orf18 solute carrier family 35 member F6 63933 CCDC90A mitochondrial calcium uniporter regulator 1 60492 CCDC90B coiled-coil domain containing 90B 64599 CDS2 GRB10 interacting GYF protein 1 1119 CHKA choline kinase alpha 1120 CHKB choline kinase beta 386593 CHKB-CPT1B CHKB-CPT1B readthrough (NMD candidate) 64174 DPEP2 dipeptidase 2 64180 DPEP3 dipeptidase 3 55500 ETNK1 ethanolamine kinase 1 55224 ETNK2 ethanolamine kinase 2 23017 FAIM2 Fas apoptotic inhibitory molecule 2 2907 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 84278 HIATL2 major facilitator superfamily domain containing 14C 81533 ITFG1 integrin alpha FG-GAP repeat containing 1 84522 JAGN1 jagunal homolog 1 100137047 JMJD7 jumonji domain containing 7 79831 KDM8 lysine demethylase 8 80168 MOGAT2 monoacylglycerol O-acyltransferase 2 25934 NIPSNAP3A nipsnap homolog 3A 5130 PCYT1A phosphate cytidylyltransferase 1, choline, alpha 9468 PCYT1B phosphate cytidylyltransferase 1, choline, beta 5833 PCYT2 phosphate cytidylyltransferase 2, ethanolamine 162466 PHOSPHO1 phosphoethanolamine/phosphocholine phosphatase 130814 PQLC3 PQ loop repeat containing 3 145270 PRIMA1 proline rich membrane anchor 1 139411 PTCHD1 patched domain containing 1 374308 PTCHD3 patched domain containing 3 442213 PTCHD4 patched domain containing 4 7803 PTP4A1 protein tyrosine phosphatase type IVA, member 1 8073 PTP4A2 protein tyrosine phosphatase type IVA, member 2 10066 SCAMP2 secretory carrier membrane protein 2 151473 SLC16A14 solute carrier family 16 member 14 7355 SLC35A2 solute carrier family 35 member A2 23443 SLC35A3 solute carrier family 35 member A3 113829 SLC35A4 solute carrier family 35 member A4 55032 SLC35A5 solute carrier family 35 member A5 347734 SLC35B2 solute carrier family 35 member B2 51000 SLC35B3 solute carrier family 35 member B3 51006 SLC35C2 solute carrier family 35 member C2 79939 SLC35E1 solute carrier family 35 member E1 9906 SLC35E2 solute carrier family 35 member E2A 55508 SLC35E3 solute carrier family 35 member E3 339665 SLC35E4 solute carrier family 35 member E4 222553 SLC35F1 solute carrier family 35 member F1 54733 SLC35F2 solute carrier family 35 member F2 80255 SLC35F5 solute carrier family 35 member F5 159371 SLC35G1 solute carrier family 35 member G1 23446 SLC44A1 solute carrier family 44 member 1 57153 SLC44A2 solute carrier family 44 member 2 126969 SLC44A3 solute carrier family 44 member 3 80736 SLC44A4 solute carrier family 44 member 4 204962 SLC44A5 solute carrier family 44 member 5 113235 SLC46A1 solute carrier family 46 member 1 283537 SLC46A3 solute carrier family 46 member 3 64114 TMBIM1 transmembrane BAX inhibitor motif containing 1 51643 TMBIM4 transmembrane BAX inhibitor motif containing 4

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 2.68e-01 2.05e-12 GO choline transmembrane transporter activity molecular_function 2.17e-01 5.13e-09 Reactome Transport of nucleotide sugars Transport of small molecules 2.06e-01 3.87e-13 Reactome Synthesis of PE Metabolism 1.21e-01 5.46e-12 GO choline transport biological_process 1.06e-01 2.20e-22 Reactome Synthesis of PC Metabolism 9.98e-02 1.40e-06 GO sialic acid transmembrane transporter activity molecular_function 6.68e-02 5.59e-22 GO phosphatidylcholine biosynthetic process biological_process 2.56e-02 1.00e-04 GO 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process biological_process 1.79e-02 1.00e-04 Reactome Transport and synthesis of PAPS Metabolism 1.34e-02 4.36e-04 GO metalloexopeptidase activity molecular_function 4.22e-03 6.02e-09 GO integral component of Golgi membrane cellular_component

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 lipid biosynthetic process 0.00e+00 0.00e+00 glycerolipid metabolic process 0.00e+00 0.00e+00 phospholipid biosynthetic process 0.00e+00 0.00e+00 glycerophospholipid metabolic process 0.00e+00 0.00e+00 phospholipid metabolic process 0.00e+00 0.00e+00 phosphatidylcholine biosynthetic process 0.00e+00 0.00e+00 phosphatidylcholine metabolic process 0.00e+00 0.00e+00 glycerophospholipid biosynthetic process 4.65e-12 4.24e-09 phosphatidylethanolamine biosynthetic process 7.57e-12 5.07e-09 choline transmembrane transporter activity 9.09e-11 7.58e-08 choline transport 1.67e-10 9.93e-08 ethanolamine kinase activity 2.24e-08 9.67e-06 ammonium transmembrane transporter activity 2.59e-08 1.11e-05 sugar:proton symporter activity 2.86e-08 1.75e-05 CDP-choline pathway 1.30e-07 4.91e-05 cation transmembrane transporter activity 1.38e-07 7.61e-05 ammonium transport 2.17e-07 7.84e-05 solute:proton symporter activity 6.56e-07 2.15e-04 sugar transmembrane transporter activity 2.74e-06 7.98e-04 nucleobase-containing compound transmembrane transporter activity

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 SYNTHESIS OF PC 0.00e+00 0.00e+00 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 0.00e+00 0.00e+00 PHOSPHOLIPID METABOLISM 0.00e+00 0.00e+00 SYNTHESIS OF PC 0.00e+00 0.00e+00 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 0.00e+00 0.00e+00 PHOSPHOLIPID METABOLISM 4.55e-12 1.77e-09 SYNTHESIS OF PE 1.03e-11 3.01e-09 SYNTHESIS OF PE 3.45e-08 7.14e-06 AMINE COMPOUND SLC TRANSPORTERS 8.55e-08 2.22e-05 AMINE COMPOUND SLC TRANSPORTERS 2.10e-07 5.25e-05 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 5.46e-06 8.53e-04 SLC MEDIATED TRANSMEMBRANE TRANSPORT 7.55e-06 1.48e-03 SLC MEDIATED TRANSMEMBRANE TRANSPORT 3.11e-05 4.30e-03 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 9.05e-05 1.42e-02 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 5.86e-04 7.40e-02 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 7.20e-04 7.47e-02 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 1.34e-02 1.00e+00 ION TRANSPORT BY P TYPE ATPASES 1.43e-02 9.78e-01 ION TRANSPORT BY P TYPE ATPASES 2.49e-02 1.00e+00 ION CHANNEL TRANSPORT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.35e-05 8.69e-02 bowed ulna 3.81e-05 1.19e-01 bowed radius 3.74e-03 1.00e+00 bowed femur 3.75e-03 1.00e+00 bowed humerus 3.75e-03 1.00e+00 bowed fibula 5.61e-03 1.00e+00 decreased tidal volume 7.47e-03 1.00e+00 decreased trophoblast glycogen cell number 9.04e-03 1.00e+00 decreased pulmonary ventilation 9.33e-03 1.00e+00 ovary hyperplasia 1.12e-02 1.00e+00 decreased brown fat cell number 1.12e-02 1.00e+00 enhanced sensorimotor gating 1.12e-02 1.00e+00 abnormal clavicle morphology 1.12e-02 1.00e+00 failure of bone ossification 1.39e-02 1.00e+00 increased physiological sensitivity to xenobiotic 1.49e-02 1.00e+00 aorta dilation 1.49e-02 1.00e+00 osteomalacia 1.68e-02 1.00e+00 abnormal sarcolemma morphology 1.86e-02 1.00e+00 abnormal maternal decidual layer morphology 1.86e-02 1.00e+00 eyelids fail to open 1.86e-02 1.00e+00 abnormal involuntary movement

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

²FDR corrected p-value (Benjamini-Hochberg)