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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod74

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod74 Module size 68 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1015 CDH16 cadherin 17 8642 CDH19 dachsous cadherin-related 1 8641 CDH20 protocadherin gamma subfamily B, 4 64405 CDH22 cadherin 22 60437 CDH26 cadherin 26 92211 CDHR1 cadherin related family member 1 222256 CDHR3 cadherin related family member 3 53841 CDHR5 cadherin related family member 5 1824 DSC3 desmocollin 2 147409 DSG4 desmoglein 4 3728 JUP junction plakoglobin 27328 PCDH11X protocadherin 11 X-linked 83259 PCDH11Y protocadherin 11 Y-linked 51294 PCDH12 protocadherin 12 65217 PCDH15 protocadherin related 15 27253 PCDH17 protocadherin 17 54510 PCDH18 protocadherin 18 57575 PCDH19 protocadherin 10 5100 PCDH8 protocadherin 8 5101 PCDH9 protocadherin 9 56147 PCDHA1 protocadherin alpha 1 56139 PCDHA10 protocadherin alpha 10 56138 PCDHA11 protocadherin alpha 11 56137 PCDHA12 protocadherin alpha 12 56136 PCDHA13 protocadherin alpha 13 56145 PCDHA3 protocadherin alpha 3 56144 PCDHA4 protocadherin alpha 4 56143 PCDHA5 protocadherin alpha 5 56142 PCDHA6 protocadherin alpha 6 56141 PCDHA7 protocadherin alpha 7 56140 PCDHA8 protocadherin alpha 8 9752 PCDHA9 protocadherin alpha 9 56135 PCDHAC1 protocadherin alpha subfamily C, 1 56134 PCDHAC2 protocadherin alpha subfamily C, 2 29930 PCDHB1 protocadherin beta 1 56126 PCDHB10 protocadherin beta 10 56125 PCDHB11 protocadherin beta 11 56124 PCDHB12 protocadherin beta 12 56123 PCDHB13 protocadherin beta 13 56121 PCDHB15 protocadherin beta 15 57717 PCDHB16 protocadherin beta 16 56133 PCDHB2 protocadherin beta 2 56132 PCDHB3 protocadherin beta 3 56131 PCDHB4 protocadherin beta 4 56130 PCDHB6 protocadherin beta 6 56129 PCDHB7 protocadherin beta 7 56128 PCDHB8 protocadherin beta 8 56114 PCDHGA1 protocadherin gamma subfamily A, 1 56106 PCDHGA10 protocadherin gamma subfamily A, 10 56105 PCDHGA11 protocadherin gamma subfamily A, 11 26025 PCDHGA12 protocadherin gamma subfamily A, 12 56113 PCDHGA2 protocadherin gamma subfamily A, 2 56112 PCDHGA3 protocadherin gamma subfamily A, 3 56111 PCDHGA4 protocadherin gamma subfamily A, 4 56110 PCDHGA5 protocadherin gamma subfamily A, 5 56109 PCDHGA6 protocadherin gamma subfamily A, 6 56108 PCDHGA7 protocadherin gamma subfamily A, 7 9708 PCDHGA8 protocadherin gamma subfamily A, 8 56107 PCDHGA9 protocadherin gamma subfamily A, 9 56104 PCDHGB1 protocadherin gamma subfamily B, 1 56103 PCDHGB2 protocadherin gamma subfamily B, 2 56102 PCDHGB3 protocadherin gamma subfamily B, 3 8641 PCDHGB4 protocadherin gamma subfamily B, 4 56100 PCDHGB6 protocadherin gamma subfamily B, 6 56099 PCDHGB7 protocadherin gamma subfamily B, 7 5098 PCDHGC3 protocadherin gamma subfamily C, 3 56098 PCDHGC4 protocadherin gamma subfamily C, 4 56097 PCDHGC5 protocadherin gamma subfamily C, 5

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 3.86e-01 8.06e-141 GO homophilic cell adhesion via plasma membrane adhesion molecules biological_process 2.02e-02 2.64e-30 GO calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules 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 cell-cell adhesion 0.00e+00 0.00e+00 cell-cell adhesion via plasma-membrane adhesion molecules 0.00e+00 0.00e+00 homophilic cell adhesion via plasma membrane adhesion molecules 0.00e+00 0.00e+00 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules 0.00e+00 0.00e+00 synapse organization 0.00e+00 0.00e+00 synapse assembly 0.00e+00 0.00e+00 chemical synaptic transmission 0.00e+00 0.00e+00 calcium ion binding 4.27e-06 1.12e-03 desmosome 1.71e-05 3.99e-03 photoreceptor cell cilium 2.54e-05 5.75e-03 cornified envelope 3.25e-05 7.19e-03 non-motile cilium 2.12e-04 3.79e-02 cell-cell junction 2.81e-04 4.88e-02 photoreceptor outer segment 8.62e-04 1.75e-01 photoreceptor cell maintenance 1.11e-03 1.60e-01 photoreceptor connecting cilium 1.32e-03 2.48e-01 cell recognition 2.16e-03 2.80e-01 ciliary transition zone 3.23e-03 5.01e-01 brain development 3.69e-03 4.33e-01 cilium

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.72e-04 3.2e-01 decreased skin tensile strength 1.87e-03 1.0e+00 acantholysis 1.87e-03 1.0e+00 abnormal heart echocardiography feature 5.63e-03 1.0e+00 abnormal paired-pulse inhibition 7.51e-03 1.0e+00 abnormal hair cortex morphology 7.51e-03 1.0e+00 hair follicle outer rooth sheath hyperplasia 9.36e-03 1.0e+00 abnormal inner hair cell kinocilium morphology 9.37e-03 1.0e+00 hair follicle degeneration 1.12e-02 1.0e+00 brittle hair 1.12e-02 1.0e+00 enlarged hair follicles 1.31e-02 1.0e+00 blistering 1.31e-02 1.0e+00 abnormal cochlear hair bundle tip links morphology 1.31e-02 1.0e+00 greasy coat 1.31e-02 1.0e+00 absent guard hair 1.31e-02 1.0e+00 abnormal hair cycle catagen phase 1.49e-02 1.0e+00 abnormal intercalated disc morphology 1.49e-02 1.0e+00 decreased synaptic depression 1.50e-02 1.0e+00 short cochlear hair cell stereocilia 1.50e-02 1.0e+00 abnormal cochlear hair cell inter-stereocilial links morphology 1.50e-02 1.0e+00 abnormal organ of Corti supporting cell morphology

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

²FDR corrected p-value (Benjamini-Hochberg)