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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod245

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod245 Module size 16 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 2647 BLOC1S1 biogenesis of lysosomal organelles complex 1 subunit 1 282991 BLOC1S2 biogenesis of lysosomal organelles complex 1 subunit 2 388552 BLOC1S3 biogenesis of lysosomal organelles complex 1 subunit 3 55330 BLOC1S4 biogenesis of lysosomal organelles complex 1 subunit 4 63915 BLOC1S5 biogenesis of lysosomal organelles complex 1 subunit 5 26258 BLOC1S6 biogenesis of lysosomal organelles complex 1 subunit 6 84062 DTNBP1 dystrobrevin binding protein 1 3257 HPS1 HPS1, biogenesis of lysosomal organelles complex 3 subunit 1 84343 HPS3 HPS3, biogenesis of lysosomal organelles complex 2 subunit 1 89781 HPS4 HPS4, biogenesis of lysosomal organelles complex 3 subunit 2 11234 HPS5 HPS5, biogenesis of lysosomal organelles complex 2 subunit 2 79803 HPS6 HPS6, biogenesis of lysosomal organelles complex 2 subunit 3 79036 KXD1 KxDL motif containing 1 8170 SLC14A2 solute carrier family 14 member 2 23557 SNAPIN SNAP associated protein 644186 SYCE3 synaptonemal complex central element protein 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 2.68e-01 3.65e-25 GO BLOC-1 complex cellular_component 1.53e-01 8.80e-22 GO anterograde synaptic vesicle transport biological_process 9.99e-02 1.09e-07 GO organelle organization biological_process 9.16e-02 5.16e-21 GO melanosome organization biological_process 2.58e-02 9.16e-12 GO lysosome localization 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 vesicle organization 0.00e+00 0.00e+00 pigmentation 0.00e+00 0.00e+00 cellular pigmentation 0.00e+00 0.00e+00 melanosome organization 0.00e+00 0.00e+00 pigment granule organization 0.00e+00 0.00e+00 anterograde axonal transport 0.00e+00 0.00e+00 axo-dendritic transport 0.00e+00 0.00e+00 organelle transport along microtubule 0.00e+00 0.00e+00 synaptic vesicle transport 0.00e+00 0.00e+00 cytoskeleton-dependent intracellular transport 0.00e+00 0.00e+00 axonal transport 0.00e+00 0.00e+00 vesicle transport along microtubule 0.00e+00 0.00e+00 transport along microtubule 0.00e+00 0.00e+00 anterograde synaptic vesicle transport 0.00e+00 0.00e+00 BLOC-1 complex 0.00e+00 0.00e+00 axon cytoplasm 0.00e+00 0.00e+00 cell projection cytoplasm 1.60e-11 8.84e-09 BORC complex 2.21e-11 1.95e-08 organelle localization 1.89e-10 1.53e-07 establishment of vesicle localization

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.31e-07 5.71e-05 GOLGI ASSOCIATED VESICLE BIOGENESIS 3.49e-07 8.38e-05 TRANS GOLGI NETWORK VESICLE BUDDING 6.24e-07 1.12e-04 GOLGI ASSOCIATED VESICLE BIOGENESIS 1.05e-06 1.81e-04 TRANS GOLGI NETWORK VESICLE BUDDING 6.28e-06 1.24e-03 MEMBRANE TRAFFICKING 6.85e-06 1.05e-03 MEMBRANE TRAFFICKING 7.26e-03 6.18e-01 AMINE COMPOUND SLC TRANSPORTERS 9.66e-03 7.80e-01 LYSOSOME VESICLE BIOGENESIS 1.80e-02 1.00e+00 AMINE COMPOUND SLC TRANSPORTERS 1.80e-02 1.00e+00 LYSOSOME VESICLE BIOGENESIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 0.00e+00 0.00e+00 increased bleeding time 0.00e+00 0.00e+00 abnormal eye pigmentation 0.00e+00 0.00e+00 decreased platelet serotonin level 0.00e+00 0.00e+00 diluted coat color 0.00e+00 0.00e+00 abnormal melanosome morphology 0.00e+00 0.00e+00 abnormal platelet dense granule number 0.00e+00 0.00e+00 decreased eye pigmentation 7.87e-12 5.66e-07 abnormal choroid pigmentation 3.21e-11 2.03e-06 decreased platelet ATP level 1.84e-09 5.70e-05 abnormal platelet physiology 5.82e-08 9.48e-04 abnormal kidney physiology 1.33e-07 1.74e-03 decreased platelet aggregation 4.44e-07 4.80e-03 decreased ear pigmentation 4.88e-07 5.14e-03 decreased lysosomal enzyme secretion 5.38e-07 5.58e-03 decreased platelet ADP level 8.08e-07 7.36e-03 abnormal ear pigmentation 1.21e-06 1.01e-02 decreased tail pigmentation 4.37e-06 2.63e-02 abnormal choroid melanin granule morphology 1.00e-05 4.72e-02 abnormal lysosome physiology 1.96e-05 7.47e-02 increased lysosomal enzyme secretion

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

²FDR corrected p-value (Benjamini-Hochberg)