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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod98

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod98 Module size 45 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10295 BCKDK branched chain ketoacid dehydrogenase kinase 8927 BSN bassoon presynaptic cytomatrix protein 26059 ERC2 ELKS/RAB6-interacting/CAST family member 2 26280 IL1RAPL2 interleukin 1 receptor accessory protein like 2 22859 LPHN1 adhesion G protein-coupled receptor L1 23266 LPHN2 adhesion G protein-coupled receptor L2 1954 MEGF8 multiple EGF like domains 8 5163 PDK1 pyruvate dehydrogenase kinase 1 5164 PDK2 pyruvate dehydrogenase kinase 2 5165 PDK3 pyruvate dehydrogenase kinase 3 5166 PDK4 pyruvate dehydrogenase kinase 4 8500 PPFIA1 PTPRF interacting protein alpha 1 8499 PPFIA2 PTPRF interacting protein alpha 2 8541 PPFIA3 PTPRF interacting protein alpha 3 8497 PPFIA4 PTPRF interacting protein alpha 4 8496 PPFIBP1 PPFIA binding protein 1 8495 PPFIBP2 PPFIA binding protein 2 5782 PTPN12 protein tyrosine phosphatase, non-receptor type 12 26469 PTPN18 protein tyrosine phosphatase, non-receptor type 18 5771 PTPN2 protein tyrosine phosphatase, non-receptor type 2 26095 PTPN20A protein tyrosine phosphatase, non-receptor type 20 11099 PTPN21 protein tyrosine phosphatase, non-receptor type 21 26191 PTPN22 protein tyrosine phosphatase, non-receptor type 22 5780 PTPN9 protein tyrosine phosphatase, non-receptor type 9 5786 PTPRA protein tyrosine phosphatase, receptor type A 5787 PTPRB protein tyrosine phosphatase, receptor type B 5788 PTPRC protein tyrosine phosphatase, receptor type C 5789 PTPRD protein tyrosine phosphatase, receptor type D 5791 PTPRE protein tyrosine phosphatase, receptor type E 5792 PTPRF protein tyrosine phosphatase, receptor type F 5793 PTPRG protein tyrosine phosphatase, receptor type G 5794 PTPRH protein tyrosine phosphatase, receptor type H 5796 PTPRK protein tyrosine phosphatase, receptor type K 5797 PTPRM protein tyrosine phosphatase, receptor type M 5798 PTPRN protein tyrosine phosphatase, receptor type N 5799 PTPRN2 protein tyrosine phosphatase, receptor type N2 5800 PTPRO protein tyrosine phosphatase, receptor type O 374462 PTPRQ protein tyrosine phosphatase, receptor type Q 5801 PTPRR protein tyrosine phosphatase, receptor type R 5802 PTPRS protein tyrosine phosphatase, receptor type S 11122 PTPRT protein tyrosine phosphatase, receptor type T 10076 PTPRU protein tyrosine phosphatase, receptor type U 5803 PTPRZ1 protein tyrosine phosphatase, receptor type Z1 64221 ROBO3 roundabout guidance receptor 3 399473 SPRED3 sprouty related EVH1 domain containing 3

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 6.60e-01 6.21e-40 GO transmembrane receptor protein tyrosine phosphatase activity molecular_function 2.91e-01 1.07e-09 GO non-membrane spanning protein tyrosine phosphatase activity molecular_function 2.84e-01 2.15e-09 GO regulation of acetyl-CoA biosynthetic process from pyruvate biological_process 2.70e-01 4.35e-22 Reactome Receptor-type tyrosine-protein phosphatases Neuronal System 5.88e-02 8.37e-11 GO presynaptic active zone cellular_component 5.58e-02 6.83e-47 GO peptidyl-tyrosine dephosphorylation biological_process 1.94e-02 7.18e-08 Reactome Acetylcholine Neurotransmitter Release Cycle Neuronal System 1.70e-02 2.19e-07 GO regulation of glucose metabolic process biological_process 5.11e-03 3.95e-35 GO protein tyrosine phosphatase activity molecular_function 3.71e-03 9.22e-08 Reactome Norepinephrine Neurotransmitter Release Cycle Neuronal System

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 protein dephosphorylation 0.00e+00 0.00e+00 dephosphorylation 0.00e+00 0.00e+00 peptidyl-tyrosine dephosphorylation 0.00e+00 0.00e+00 hydrolase activity, acting on ester bonds 0.00e+00 0.00e+00 phosphoprotein phosphatase activity 0.00e+00 0.00e+00 protein tyrosine phosphatase activity 0.00e+00 0.00e+00 phosphatase activity 0.00e+00 0.00e+00 phosphoric ester hydrolase activity 0.00e+00 0.00e+00 transmembrane receptor protein tyrosine phosphatase activity 1.05e-11 6.97e-09 pyruvate dehydrogenase (acetyl-transferring) kinase activity 2.96e-09 1.25e-06 presynaptic active zone 2.37e-08 1.47e-05 transmembrane receptor protein tyrosine phosphatase signaling pathway 2.39e-08 1.48e-05 enzyme linked receptor protein signaling pathway 4.33e-08 1.77e-05 non-membrane spanning protein tyrosine phosphatase activity 3.76e-07 1.93e-04 regulation of acetyl-CoA biosynthetic process from pyruvate 5.56e-07 2.77e-04 regulation of acyl-CoA biosynthetic process 2.16e-06 5.98e-04 presynapse 3.28e-06 1.41e-03 glutamate secretion 2.63e-05 9.14e-03 regulation of glucose metabolic process 4.05e-05 1.34e-02 glucose homeostasis

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.89e-07 4.74e-05 REGULATION OF PYRUVATE DEHYDROGENASE PDH COMPLEX 4.43e-07 1.05e-04 PYRUVATE METABOLISM 4.87e-07 8.92e-05 REGULATION OF PYRUVATE DEHYDROGENASE PDH COMPLEX 6.44e-07 1.15e-04 PYRUVATE METABOLISM 3.27e-06 6.75e-04 PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE 4.71e-06 7.44e-04 PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE 1.34e-05 1.96e-03 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 9.44e-05 1.47e-02 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 9.85e-03 7.24e-01 PHOSPHORYLATION OF CD3 AND TCR ZETA CHAINS 1.88e-02 1.00e+00 REGULATION OF IFNG SIGNALING 2.55e-02 1.00e+00 PHOSPHORYLATION OF CD3 AND TCR ZETA CHAINS 3.10e-02 1.00e+00 AXON GUIDANCE 3.84e-02 1.00e+00 SIGNALING BY ROBO RECEPTOR 3.89e-02 1.00e+00 SEMA4D IN SEMAPHORIN SIGNALING 4.72e-02 1.00e+00 REGULATION OF IFNG SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.03e-04 3.52e-01 abnormal B cell number 3.21e-04 4.69e-01 abnormal T cell subpopulation ratio 4.51e-04 5.70e-01 decreased follicular B cell number 8.34e-04 8.12e-01 abnormal central nervous system regeneration 1.03e-03 9.16e-01 abnormal T cell differentiation 1.20e-03 1.00e+00 abnormal positive T cell selection 1.48e-03 1.00e+00 abnormal retinal rod cell morphology 2.84e-03 1.00e+00 abnormal oligodendrocyte morphology 4.15e-03 1.00e+00 abnormal double-positive T cell morphology 4.29e-03 1.00e+00 abnormal thymocyte activation 4.41e-03 1.00e+00 decreased mature B cell number 5.01e-03 1.00e+00 increased exploration in new environment 5.55e-03 1.00e+00 abnormal T cell morphology 5.61e-03 1.00e+00 abnormal glycerol level 5.88e-03 1.00e+00 abnormal synaptic vesicle number 5.91e-03 1.00e+00 abnormal B cell activation 5.98e-03 1.00e+00 spleen hyperplasia 6.01e-03 1.00e+00 increased interleukin-12 secretion 6.61e-03 1.00e+00 increased B cell number 6.83e-03 1.00e+00 increased memory T cell number

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

²FDR corrected p-value (Benjamini-Hochberg)