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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod320

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod320 Module size 39 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 25999 CLIP3 CAP-Gly domain containing linker protein 3 53347 CLIP4 ubiquitin associated and SH3 domain containing A 201625 DNAH12 dynein axonemal heavy chain 12 154288 KHDC3L KH domain containing 3 like, subcortical maternal complex member 3832 KIF11 kinesin family member 11 113220 KIF12 kinesin family member 12 63971 KIF13A kinesin family member 13A 23303 KIF13B kinesin family member 13B 9928 KIF14 kinesin family member 14 56992 KIF15 kinesin family member 15 55614 KIF16B kinesin family member 16B 57576 KIF17 kinesin family member 17 124602 KIF19 kinesin family member 19 547 KIF1A kinesin family member 1A 305967 KIF1B kinesin family member 13B 10749 KIF1C kinesin family member 1C 9585 KIF20B kinesin family member 20B 55605 KIF21A kinesin family member 21A 23046 KIF21B kinesin family member 21B 3835 KIF22 kinesin family member 22 347240 KIF24 kinesin family member 24 3834 KIF25 kinesin family member 25 55083 KIF26B kinesin family member 26B 55582 KIF27 kinesin family member 27 11127 KIF3A kinesin family member 3A 9371 KIF3B kinesin family member 3B 3797 KIF3C kinesin family member 3C 285643 KIF4B kinesin family member 4B 3798 KIF5A kinesin family member 5A 3800 KIF5C kinesin family member 5C 221458 KIF6 kinesin family member 6 374654 KIF7 kinesin family member 7 64147 KIF9 kinesin family member 9 3833 KIFC1 kinesin family member C1 90990 KIFC2 kinesin family member C2 3801 KIFC3 kinesin family member C3 10982 MAPRE2 microtubule associated protein RP/EB family member 2 22924 MAPRE3 microtubule associated protein RP/EB family member 3 57519 STARD9 StAR related lipid transfer domain containing 9

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 2.78e-01 2.78e-80 GO kinesin complex cellular_component 1.01e-01 1.36e-82 GO microtubule motor activity molecular_function 8.74e-02 1.07e-79 GO microtubule-based movement biological_process 7.13e-02 1.09e-06 GO protein localization to microtubule biological_process 6.16e-02 2.01e-29 GO ATP-dependent microtubule motor activity, plus-end-directed molecular_function 4.67e-02 2.79e-63 Reactome Kinesins Hemostasis

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 microtubule-based movement 0.00e+00 0.00e+00 microtubule-based process 0.00e+00 0.00e+00 cytoskeleton-dependent intracellular transport 0.00e+00 0.00e+00 transport along microtubule 0.00e+00 0.00e+00 retrograde vesicle-mediated transport, Golgi to ER 0.00e+00 0.00e+00 supramolecular fiber 0.00e+00 0.00e+00 kinesin complex 0.00e+00 0.00e+00 microtubule associated complex 0.00e+00 0.00e+00 microtubule 0.00e+00 0.00e+00 ATPase activity 0.00e+00 0.00e+00 tubulin binding 0.00e+00 0.00e+00 microtubule motor activity 0.00e+00 0.00e+00 nucleoside-triphosphatase activity 0.00e+00 0.00e+00 microtubule binding 0.00e+00 0.00e+00 motor activity 0.00e+00 0.00e+00 ATP-dependent microtubule motor activity, plus-end-directed 9.11e-11 7.59e-08 antigen processing and presentation of exogenous peptide antigen via MHC class II 9.72e-11 8.08e-08 antigen processing and presentation of peptide antigen via MHC class II 9.72e-11 8.08e-08 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 3.79e-10 2.97e-07 Golgi vesicle transport

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 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 0.00e+00 0.00e+00 KINESINS 0.00e+00 0.00e+00 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 0.00e+00 0.00e+00 MHC CLASS II ANTIGEN PRESENTATION 0.00e+00 0.00e+00 KINESINS 2.66e-11 1.01e-08 MHC CLASS II ANTIGEN PRESENTATION 1.28e-03 1.25e-01 ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS 2.18e-03 2.30e-01 ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS 4.61e-03 3.84e-01 PROTEIN FOLDING 5.05e-03 4.61e-01 PROTEIN FOLDING 6.37e-03 5.57e-01 RECYCLING PATHWAY OF L1 2.21e-02 1.00e+00 RECYCLING PATHWAY OF L1 3.00e-02 1.00e+00 L1CAM INTERACTIONS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.36e-06 3.40e-02 abnormal spinal cord morphology 6.31e-05 1.66e-01 hydroencephaly 3.48e-04 4.89e-01 abnormal vesicle-mediated transport 3.80e-04 5.19e-01 decreased brain size 4.03e-04 5.35e-01 unresponsive to tactile stimuli 6.18e-04 6.84e-01 absent embryonic cilia 1.28e-03 1.00e+00 abnormal axonal transport 2.62e-03 1.00e+00 abnormal direction of heart looping 2.93e-03 1.00e+00 thin cerebral cortex 3.08e-03 1.00e+00 microcephaly 3.75e-03 1.00e+00 myocardium hypoplasia 4.55e-03 1.00e+00 partial embryonic lethality before implantation 4.79e-03 1.00e+00 abnormal synaptic vesicle number 5.03e-03 1.00e+00 abnormal left-right axis patterning 5.61e-03 1.00e+00 abnormal central tendon morphology 6.03e-03 1.00e+00 abnormal hippocampus morphology 6.13e-03 1.00e+00 distended pericardium 6.94e-03 1.00e+00 exencephaly 8.37e-03 1.00e+00 incomplete embryo turning 9.34e-03 1.00e+00 pulmonary artery hypoplasia

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

²FDR corrected p-value (Benjamini-Hochberg)