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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod26

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod26 Module size 55 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 219681 ARMC3 armadillo repeat containing 3 8537 BCAS1 breast carcinoma amplified sequence 1 23299 BICD2 BICD cargo adaptor 2 283461 C12orf40 chromosome 12 open reading frame 40 26074 C20orf26 cilia and flagella associated protein 61 93233 CCDC114 coiled-coil domain containing 114 115948 CCDC151 coiled-coil domain containing 151 348807 CCDC37 cilia and flagella associated protein 100 160762 CCDC63 coiled-coil domain containing 63 1639 DCTN1 dynactin subunit 1 10540 DCTN2 dynactin subunit 2 51164 DCTN4 dynactin subunit 4 84516 DCTN5 dynactin subunit 5 10671 DCTN6 dynactin subunit 6 25981 DNAH1 dynein axonemal heavy chain 1 196385 DNAH10 dynein axonemal heavy chain 10 8701 DNAH11 dynein axonemal heavy chain 11 127602 DNAH14 dynein axonemal heavy chain 14 8632 DNAH17 dynein axonemal heavy chain 17 146754 DNAH2 dynein axonemal heavy chain 2 55567 DNAH3 dynein axonemal heavy chain 3 1767 DNAH5 dynein axonemal heavy chain 5 1768 DNAH6 dynein axonemal heavy chain 6 56171 DNAH7 dynein axonemal heavy chain 7 1769 DNAH8 dynein axonemal heavy chain 8 1770 DNAH9 dynein axonemal heavy chain 9 27019 DNAI1 dynein axonemal intermediate chain 1 64446 DNAI2 dynein axonemal intermediate chain 2 10126 DNAL4 dynein axonemal light chain 4 7802 DNALI1 dynein axonemal light intermediate chain 1 144132 DNHD1 dynein heavy chain domain 1 1778 DYNC1H1 dynein cytoplasmic 1 heavy chain 1 1780 DYNC1I1 dynein cytoplasmic 1 intermediate chain 1 51143 DYNC1LI1 dynein cytoplasmic 1 light intermediate chain 1 1783 DYNC1LI2 dynein cytoplasmic 1 light intermediate chain 2 79659 DYNC2H1 dynein cytoplasmic 2 heavy chain 1 51626 DYNC2LI1 dynein cytoplasmic 2 light intermediate chain 1 8655 DYNLL1 dynein light chain LC8-type 1 140735 DYNLL2 dynein light chain LC8-type 2 83658 DYNLRB1 dynein light chain roadblock-type 1 83657 DYNLRB2 dynein light chain roadblock-type 2 6993 DYNLT1 dynein light chain Tctex-type 1 6990 DYNLT3 dynein light chain Tctex-type 3 24139 EML2 echinoderm microtubule associated protein like 2 161829 EXD1 exonuclease 3'-5' domain containing 1 94086 HSPB9 heat shock protein family B (small) member 9 114876 OSBPL1A oxysterol binding protein like 1A 128344 PIFO primary cilia formation 287531 RILP Rab interacting lysosomal protein 9728 SECISBP2L SECIS binding protein 2 like 8723 SNX4 sorting nexin 4 132671 SPATA18 spermatogenesis associated 18 6991 TCTE3 t-complex-associated-testis-expressed 3 55112 WDR60 WD repeat domain 60 93594 WDR67 TBC1 domain family member 31

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 3.51e-01 3.62e-65 GO dynein complex cellular_component 2.96e-01 5.90e-33 GO cytoplasmic dynein complex cellular_component 2.28e-01 2.58e-17 GO outer dynein arm cellular_component 2.03e-01 8.42e-41 GO ATP-dependent microtubule motor activity, minus-end-directed molecular_function 1.58e-01 4.75e-47 GO dynein light intermediate chain binding molecular_function 1.30e-01 6.14e-09 GO dynactin complex cellular_component 6.66e-02 2.00e-23 Reactome COPI-independent Golgi-to-ER retrograde traffic Vesicle-mediated transport 4.69e-02 3.54e-14 GO outer dynein arm assembly biological_process 4.53e-02 1.48e-47 GO dynein intermediate chain binding molecular_function 1.06e-02 6.90e-15 GO cilium movement 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 0e+00 0e+00 organelle assembly 0e+00 0e+00 outer dynein arm assembly 0e+00 0e+00 cilium assembly 0e+00 0e+00 cell projection assembly 0e+00 0e+00 axoneme assembly 0e+00 0e+00 microtubule cytoskeleton organization 0e+00 0e+00 cilium movement 0e+00 0e+00 microtubule-based movement 0e+00 0e+00 microtubule-based process 0e+00 0e+00 cilium organization 0e+00 0e+00 axonemal dynein complex assembly 0e+00 0e+00 cytoskeleton-dependent intracellular transport 0e+00 0e+00 transport along microtubule 0e+00 0e+00 antigen processing and presentation of peptide antigen 0e+00 0e+00 antigen processing and presentation 0e+00 0e+00 antigen processing and presentation of exogenous peptide antigen via MHC class II 0e+00 0e+00 antigen processing and presentation of peptide antigen via MHC class II 0e+00 0e+00 ER to Golgi vesicle-mediated transport 0e+00 0e+00 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 0e+00 0e+00 cilium or flagellum-dependent cell motility

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 MHC CLASS II ANTIGEN PRESENTATION 0.00e+00 0.00e+00 MHC CLASS II ANTIGEN PRESENTATION 8.56e-07 1.95e-04 LOSS OF NLP FROM MITOTIC CENTROSOMES 1.54e-06 3.37e-04 RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES 2.31e-06 4.89e-04 MITOTIC G2 G2 M PHASES 3.26e-06 5.25e-04 LOSS OF NLP FROM MITOTIC CENTROSOMES 3.96e-06 6.30e-04 RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES 5.54e-06 8.64e-04 MITOTIC G2 G2 M PHASES 4.14e-05 7.07e-03 ACTIVATION OF BH3 ONLY PROTEINS 7.79e-05 1.24e-02 INTRINSIC PATHWAY FOR APOPTOSIS 1.58e-04 1.92e-02 ACTIVATION OF BH3 ONLY PROTEINS 2.31e-04 2.70e-02 INTRINSIC PATHWAY FOR APOPTOSIS 2.88e-04 3.95e-02 CELL CYCLE MITOTIC 1.21e-03 1.39e-01 RETROGRADE NEUROTROPHIN SIGNALLING 1.27e-03 1.44e-01 CELL CYCLE 3.83e-03 3.66e-01 APOPTOSIS 4.46e-03 3.73e-01 RETROGRADE NEUROTROPHIN SIGNALLING 6.60e-03 5.22e-01 APOPTOSIS 2.71e-02 1.00e+00 NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE 3.73e-02 1.00e+00 NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.83e-10 9.09e-06 situs inversus totalis 2.10e-08 4.29e-04 dextrocardia 2.53e-08 4.98e-04 immotile respiratory cilia 1.10e-07 1.52e-03 micrognathia 6.98e-07 6.77e-03 left pulmonary isomerism 7.30e-07 7.02e-03 abdominal situs inversus 1.82e-06 1.37e-02 dual inferior vena cava 3.15e-06 2.07e-02 abdominal situs ambiguus 4.05e-06 2.47e-02 abnormal motile primary cilium morphology 4.97e-06 2.93e-02 abnormal left-right axis patterning 7.21e-06 3.69e-02 duplex kidney 7.60e-06 3.87e-02 abnormal respiratory motile cilium physiology 1.03e-05 4.78e-02 right-sided stomach 1.47e-05 6.11e-02 abnormal inferior vena cava morphology 3.96e-05 1.23e-01 biventricular, discordant atrioventricular connection 4.47e-05 1.32e-01 situs inversus with levocardia 4.95e-05 1.41e-01 superior-inferior ventricles 5.80e-05 1.58e-01 heterotaxia 6.64e-05 1.72e-01 double outlet right ventricle 8.41e-05 2.03e-01 abnormal motile primary cilium physiology

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

²FDR corrected p-value (Benjamini-Hochberg)