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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod119

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod119 Module size 50 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 84920 ALG10 ALG10, alpha-1,2-glucosyltransferase 144245 ALG10B ALG10B, alpha-1,2-glucosyltransferase 79087 ALG12 ALG12, alpha-1,6-mannosyltransferase 79053 ALG8 ALG8, alpha-1,3-glucosyltransferase 79796 ALG9 ALG9, alpha-1,2-mannosyltransferase 746 C11orf10 transmembrane protein 258 125972 CALR3 calreticulin 3 441549 CDNF cerebral dopamine neurotrophic factor 285888 CNPY1 canopy FGF signaling regulator 1 10330 CNPY2 canopy FGF signaling regulator 2 1603 DAD1 defender against cell death 1 84572 GNPTG N-acetylglucosamine-1-phosphate transferase subunit gamma 81502 HM13 histocompatibility minor 13 200185 KRTCAP2 keratinocyte associated protein 2 3998 LMAN1 lectin, mannose binding 1 79748 LMAN1L lectin, mannose binding 1 like 10960 LMAN2 lectin, mannose binding 2 81562 LMAN2L lectin, mannose binding 2 like 84061 MAGT1 magnesium transporter 1 7873 MANF mesencephalic astrocyte derived neurotrophic factor 90411 MCFD2 multiple coagulation factor deficiency 2 7841 MOGS mannosyl-oligosaccharide glucosidase 23420 NOMO1 NODAL modulator 1 283820 NOMO2 NODAL modulator 2 408050 NOMO3 NODAL modulator 3 100128731 OST4 oligosaccharyltransferase complex subunit 4, non-catalytic 58505 OSTC oligosaccharyltransferase complex non-catalytic subunit 5032 P2RY11 purinergic receptor P2Y11 29254 PGAP1 monoglyceride lipase 10585 POMT1 protein O-mannosyltransferase 1 29954 POMT2 protein O-mannosyltransferase 2 11079 RER1 retention in endoplasmic reticulum sorting receptor 1 7095 SEC62 SEC62 homolog, preprotein translocation factor 387923 SERP2 stress associated endoplasmic reticulum protein family member 2 7922 SLC39A7 solute carrier family 39 member 7 121665 SPPL3 signal peptide peptidase like 3 6748 SSR4 signal sequence receptor subunit 4 3703 STT3A STT3A, catalytic subunit of the oligosaccharyltransferase complex 201595 STT3B STT3B, catalytic subunit of the oligosaccharyltransferase complex 100912008 SURF4 uncharacterized LOC100912008 11018 TMED1 transmembrane p24 trafficking protein 1 10972 TMED10 transmembrane p24 trafficking protein 10 10959 TMED2 transmembrane p24 trafficking protein 2 222068 TMED4 transmembrane p24 trafficking protein 4 146456 TMED6 transmembrane p24 trafficking protein 6 54732 TMED9 transmembrane p24 trafficking protein 9 55161 TMEM33 transmembrane protein 33 133022 TRAM1L1 translocation associated membrane protein 1 like 1 9697 TRAM2 translocation associated membrane protein 2 7991 TUSC3 tumor suppressor candidate 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 5.28e-01 2.75e-19 GO oligosaccharyltransferase complex cellular_component 1.95e-01 2.42e-10 GO dolichol-linked oligosaccharide biosynthetic process biological_process 9.69e-02 1.09e-04 GO integral component of cytoplasmic side of endoplasmic reticulum membrane cellular_component 9.51e-02 8.89e-18 GO COPII-coated ER to Golgi transport vesicle cellular_component 5.37e-02 2.92e-12 Reactome Cargo concentration in the ER Metabolism of proteins#Vesicle-mediated transport 5.09e-02 1.05e-18 GO endoplasmic reticulum-Golgi intermediate compartment cellular_component 3.86e-02 5.39e-06 GO early endosome to Golgi transport biological_process 2.95e-02 6.84e-06 GO mannosyltransferase activity molecular_function 2.47e-02 3.47e-07 GO mannose binding molecular_function 1.53e-02 1.53e-04 GO aspartic endopeptidase activity, intramembrane cleaving molecular_function 1.23e-02 2.19e-15 GO endoplasmic reticulum-Golgi intermediate compartment membrane cellular_component 1.06e-02 1.41e-14 GO Golgi organization biological_process 5.61e-03 8.25e-07 GO endoplasmic reticulum organization 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 0.00e+00 0.00e+00 glycosylation 0.00e+00 0.00e+00 glycoprotein biosynthetic process 0.00e+00 0.00e+00 glycoprotein metabolic process 0.00e+00 0.00e+00 protein glycosylation 0.00e+00 0.00e+00 macromolecule glycosylation 0.00e+00 0.00e+00 protein N-linked glycosylation 0.00e+00 0.00e+00 protein N-linked glycosylation via asparagine 0.00e+00 0.00e+00 endoplasmic reticulum-Golgi intermediate compartment 0.00e+00 0.00e+00 endoplasmic reticulum-Golgi intermediate compartment membrane 0.00e+00 0.00e+00 oligosaccharyltransferase complex 0.00e+00 0.00e+00 transferase activity, transferring glycosyl groups 0.00e+00 0.00e+00 transferase activity, transferring hexosyl groups 5.26e-12 3.55e-09 dolichyl-diphosphooligosaccharide-protein glycotransferase activity 1.03e-11 6.85e-09 oligosaccharyl transferase activity 1.65e-08 1.04e-05 dolichol-linked oligosaccharide biosynthetic process 2.34e-08 1.45e-05 oligosaccharide-lipid intermediate biosynthetic process 5.24e-08 3.09e-05 mannosylation 9.24e-08 5.24e-05 COPI coating of Golgi vesicle 9.24e-08 5.24e-05 COPI-coated vesicle budding 1.18e-07 4.48e-05 mannosyltransferase 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 ASPARAGINE N LINKED GLYCOSYLATION 0.00e+00 0.00e+00 POST TRANSLATIONAL PROTEIN MODIFICATION 0.00e+00 0.00e+00 ASPARAGINE N LINKED GLYCOSYLATION 0.00e+00 0.00e+00 POST TRANSLATIONAL PROTEIN MODIFICATION 8.17e-08 2.13e-05 BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN 9.27e-08 1.81e-05 BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN 2.15e-03 1.98e-01 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 2.19e-03 2.31e-01 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 6.87e-03 5.92e-01 P2Y RECEPTORS 1.51e-02 1.00e+00 NUCLEOTIDE LIKE PURINERGIC RECEPTORS 2.44e-02 1.00e+00 ZINC TRANSPORTERS 2.63e-02 1.00e+00 N GLYCAN TRIMMING IN THE ER AND CALNEXIN CALRETICULIN CYCLE 3.55e-02 1.00e+00 P2Y RECEPTORS 4.28e-02 1.00e+00 PRE NOTCH PROCESSING IN GOLGI 4.42e-02 1.00e+00 PRE NOTCH PROCESSING IN GOLGI 4.53e-02 1.00e+00 ZINC TRANSPORTERS 4.72e-02 1.00e+00 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.79e-04 3.26e-01 abnormal Reichert's membrane morphology 1.39e-03 1.00e+00 caudal body truncation 1.87e-03 1.00e+00 truncated foregut 1.87e-03 1.00e+00 proboscis 1.87e-03 1.00e+00 abnormal medial nasal prominence morphology 3.74e-03 1.00e+00 delayed chorioallantoic fusion 3.75e-03 1.00e+00 cyclopia 5.61e-03 1.00e+00 fused first pharyngeal arch 5.61e-03 1.00e+00 absent Rathke's pouch 7.47e-03 1.00e+00 absent cochlear microphonics 7.47e-03 1.00e+00 abnormal oropharynx morphology 7.47e-03 1.00e+00 ocular hypotelorism 9.33e-03 1.00e+00 increased Reichert's membrane thickness 9.34e-03 1.00e+00 abnormal tail bud morphology 9.35e-03 1.00e+00 abnormal scapula morphology 1.12e-02 1.00e+00 delayed somite formation 1.12e-02 1.00e+00 failure of blastocyst formation 1.12e-02 1.00e+00 abnormal parietal endoderm morphology 1.13e-02 1.00e+00 small tail bud 1.17e-02 1.00e+00 decreased lean body mass

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

²FDR corrected p-value (Benjamini-Hochberg)