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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod199

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod199 Module size 51 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 214 ALCAM activated leukocyte cell adhesion molecule 403314 APOBEC4 apolipoprotein B mRNA editing enzyme catalytic polypeptide like 4 923 CD6 CD6 molecule 140578 CHODL chondrolectin 1627 DBN1 drebrin 1 1889 ECE1 endothelin converting enzyme 1 9718 ECE2 endothelin converting enzyme 2 9427 ECEL1 endothelin converting enzyme like 1 2012 EMP1 epithelial membrane protein 1 83953 FCAMR Fc fragment of IgA and IgM receptor 54834 GDAP2 ganglioside induced differentiation associated protein 2 389400 GFRAL GDNF family receptor alpha like 199720 GGN gametogenetin 449520 GGNBP1 gametogenetin binding protein 1 (pseudogene) 79893 GGNBP2 gametogenetin binding protein 2 83606 GUCD1 guanylyl cyclase domain containing 1 2994 GYPB glycophorin B (MNS blood group) 9455 HOMER2 homer scaffold protein 2 3543 IGLL1 immunoglobulin lambda like polypeptide 1 3792 KEL Kell metallo-endopeptidase (Kell blood group) 3956 LGALS1 galectin 1 3958 LGALS3 galectin 3 3982 LIM2 lens intrinsic membrane protein 2 28992 MACROD1 MACRO domain containing 1 140733 MACROD2 MACRO domain containing 2 4311 MME membrane metalloendopeptidase 79258 MMEL1 membrane metalloendopeptidase like 1 4359 MPZ myelin protein zero 9019 MPZL1 myelin protein zero like 1 4653 MYOC myocilin 4880 NPPC natriuretic peptide C 79627 OGFRL1 opioid growth factor receptor like 1 5251 PHEX phosphate regulating endopeptidase homolog X-linked 5790 PTPRCAP protein tyrosine phosphatase, receptor type C associated protein 5768 QSOX1 quiescin sulfhydryl oxidase 1 6005 RHAG Rh associated glycoprotein 51458 RHCG Rh family C glycoprotein 305584 RHD REL proto-oncogene, NF-kB subunit 23410 SIRT3 sirtuin 3 23409 SIRT4 sirtuin 4 23408 SIRT5 sirtuin 5 51548 SIRT6 sirtuin 6 85027 SMIM3 small integral membrane protein 3 56241 SUSD2 sushi domain containing 2 55266 TMEM19 transmembrane protein 19 147744 TMEM190 transmembrane protein 190 23555 TSPAN15 tetraspanin 15 7441 VPREB1 V-set pre-B cell surrogate light chain 1 29802 VPREB3 V-set pre-B cell surrogate light chain 3 259239 WFDC11 WAP four-disulfide core domain 11 7504 XK X-linked Kx blood group

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 4.18e-01 4.62e-10 GO NAD-dependent protein deacetylase activity molecular_function 2.58e-01 1.75e-05 Reactome Rhesus glycoproteins mediate ammonium transport. Transport of small molecules 8.50e-02 7.55e-07 GO ammonium transmembrane transporter activity molecular_function 2.79e-02 7.32e-03 Reactome RUNX2 regulates genes involved in differentiation of myeloid cells Gene expression (Transcription)

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 1.64e-08 7.24e-06 metalloendopeptidase activity 3.89e-08 1.60e-05 NAD+ binding 2.56e-07 1.35e-04 protein ADP-ribosylation 4.39e-07 1.49e-04 metallopeptidase activity 4.41e-07 1.50e-04 NAD+ ADP-ribosyltransferase activity 6.42e-06 1.74e-03 deacetylase activity 8.38e-06 2.22e-03 transferase activity, transferring pentosyl groups 1.30e-05 3.31e-03 NAD binding 1.65e-05 6.06e-03 ammonium transmembrane transport 2.10e-05 7.49e-03 organic cation transport 2.41e-05 8.46e-03 protein deacetylation 3.43e-05 8.06e-03 ammonium transmembrane transporter activity 6.22e-05 1.37e-02 endopeptidase activity 6.79e-05 2.09e-02 regulation of axon diameter 7.76e-05 2.35e-02 peptidyl-lysine deacetylation 1.19e-04 3.39e-02 cellular magnesium ion homeostasis 1.30e-04 3.65e-02 peptide hormone processing 1.58e-04 2.93e-02 immunological synapse 1.85e-04 4.91e-02 positive regulation of dendritic cell differentiation 2.18e-04 5.63e-02 ammonium transport

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 9.12e-06 1.37e-03 AMINE COMPOUND SLC TRANSPORTERS 1.37e-04 2.06e-02 AMINE COMPOUND SLC TRANSPORTERS 1.35e-03 1.31e-01 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 5.19e-03 4.23e-01 ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING 5.93e-03 5.26e-01 ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING 1.09e-02 8.53e-01 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 1.29e-02 9.02e-01 SLC MEDIATED TRANSMEMBRANE TRANSPORT 4.74e-02 1.00e+00 L1CAM INTERACTIONS 4.91e-02 1.00e+00 SLC MEDIATED TRANSMEMBRANE TRANSPORT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.93e-04 3.41e-01 decreased myelin sheath thickness 2.26e-04 3.76e-01 abnormal internode morphology 1.13e-03 9.65e-01 decreased circulating potassium level 1.22e-03 1.00e+00 abnormal long bone epiphyseal plate morphology 2.35e-03 1.00e+00 disorganized long bone epiphyseal plate 2.71e-03 1.00e+00 short fibula 3.52e-03 1.00e+00 abnormal erythrocyte physiology 3.70e-03 1.00e+00 increased mean corpuscular hemoglobin concentration 3.91e-03 1.00e+00 increased circulating iron level 4.50e-03 1.00e+00 decreased cranium height 7.01e-03 1.00e+00 abnormal social/conspecific interaction 7.07e-03 1.00e+00 decreased width of hypertrophic chondrocyte zone 7.50e-03 1.00e+00 delayed muscle development 7.52e-03 1.00e+00 abnormal osteoid morphology 8.34e-03 1.00e+00 liver fibrosis 8.94e-03 1.00e+00 impaired cued conditioning behavior 9.34e-03 1.00e+00 abnormal cocaine consumption 1.11e-02 1.00e+00 abnormal lymphopoiesis 1.12e-02 1.00e+00 absent right subclavian artery 1.12e-02 1.00e+00 abnormal Harderian gland pigmentation

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

²FDR corrected p-value (Benjamini-Hochberg)