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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod69

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod69 Module size 78 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 11216 AKAP10 A-kinase anchoring protein 10 321 APBA2 amyloid beta precursor protein binding family A member 2 22903 BTBD3 BTB domain containing 3 26098 C10orf137 erythroid differentiation regulatory factor 1 256329 C11orf35 lamin tail domain containing 2 140711 C20orf118 TBC/LysM-associated domain containing 2 128653 C20orf141 chromosome 20 open reading frame 141 116349 C5orf55 EXOC3 antisense RNA 1 57091 CASS4 Cas scaffold protein family member 4 203260 CCDC107 coiled-coil domain containing 107 8476 CDC42BPA CDC42 binding protein kinase alpha 64072 CDH23 cadherin related 23 119467 CLRN3 clarin 3 1459 CSNK2A1 casein kinase 2 alpha 2 30848 CTAG2 cancer/testis antigen 2 8727 CTNNAL1 catenin alpha like 1 8642 DCHS1 dachsous cadherin-related 1 9201 DCLK1 doublecortin like kinase 1 728358 DEFA1B defensin alpha 1B 1830 DSG3 desmoglein 3 1834 DSP dentin sialophosphoprotein 64123 ELTD1 adhesion G protein-coupled receptor L4 285203 EOGT EGF domain specific O-linked N-acetylglucosamine transferase 284656 EPHA10 EPH receptor A10 100526773 EPPIN-WFDC6 EPPIN-WFDC6 readthrough 374393 FAM111B family with sequence similarity 111 member B 171482 FAM9A family with sequence similarity 9 member A 2195 FAT1 FAT atypical cadherin 1 120114 FAT3 FAT atypical cadherin 3 80206 FHOD3 formin homology 2 domain containing 3 51024 FIS1 fission, mitochondrial 1 29915 HCFC2 host cell factor C2 3092 HIP1 huntingtin interacting protein 1 9026 HIP1R huntingtin interacting protein 1 related 160492 IFLTD1 lamin tail domain containing 1 389124 IQCF5 IQ motif containing F5 9703 KIAA0100 KIAA0100 158405 KIAA1958 KIAA1958 375612 LHFPL3 LHFPL tetraspan subfamily member 3 23101 MCF2L2 MCF.2 cell line derived transforming sequence-like 2 399664 MEX3D mex-3 RNA binding family member D 51444 NARF ring finger protein 138 64428 NARFL cytosolic iron-sulfur assembly component 3 63941 NECAB3 N-terminal EF-hand calcium binding protein 3 374354 NHLRC2 NHL repeat containing 2 266553 OFCC1 orofacial cleft 1 candidate 1 8473 OGT O-linked N-acetylglucosamine (GlcNAc) transferase 55074 OXR1 oxidation resistance 1 142 PARP1 poly(ADP-ribose) polymerase 1 143 PARP4 poly(ADP-ribose) polymerase family member 4 9124 PDLIM1 PDZ and LIM domain 1 64236 PDLIM2 PDZ and LIM domain 2 27295 PDLIM3 PDZ and LIM domain 3 8572 PDLIM4 PDZ and LIM domain 4 10158 PDZK1IP1 PDZK1 interacting protein 1 10531 PITRM1 pitrilysin metallopeptidase 1 5669 PSG1 pregnancy specific beta-1-glycoprotein 1 5813 PURA purine rich element binding protein A 5814 PURB purine rich element binding protein B 642636 RAD21L1 RAD21 cohesin complex component like 1 55680 RUFY2 RUN and FYVE domain containing 2 11196 SEC23IP SEC23 interacting protein 84727 SPSB2 splA/ryanodine receptor domain and SOCS box containing 2 6769 STAC SH3 and cysteine rich domain 91683 SYT12 synaptotagmin 12 6996 TDG thymine DNA glycosylase 157378 TMEM65 transmembrane protein 65 57690 TNRC6C trinucleotide repeat containing 6C 79573 TTC13 tetratricopeptide repeat domain 13 140870 WFDC6 WAP four-disulfide core domain 6 23390 ZDHHC17 zinc finger DHHC-type containing 17 94039 ZNF101 zinc finger protein 101 7564 ZNF16 zinc finger protein 16 7767 ZNF224 zinc finger protein 224 84449 ZNF333 zinc finger protein 333 54811 ZNF562 zinc finger protein 562 9640 ZNF592 zinc finger protein 592 7553 ZNF7 zinc finger protein 7

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 3.39e-01 3.01e-05 GO protein N-acetylglucosaminyltransferase activity molecular_function 1.53e-01 1.00e-04 GO CIA complex cellular_component 3.75e-02 3.57e-04 GO clathrin light chain binding molecular_function 2.02e-02 5.44e-04 Reactome Apoptotic cleavage of cell adhesion proteins Programmed Cell Death 1.18e-02 5.44e-04 GO clathrin adaptor activity molecular_function 1.18e-02 5.44e-04 GO actin cortical patch cellular_component

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 8.74e-05 1.85e-02 protein N-acetylglucosaminyltransferase activity 2.02e-04 3.80e-02 clathrin light chain binding 2.89e-04 7.12e-02 positive regulation of platelet-derived growth factor receptor signaling pathway 4.14e-04 9.60e-02 homophilic cell adhesion via plasma membrane adhesion molecules 5.23e-04 1.16e-01 cell-cell adhesion 7.24e-04 1.16e-01 clathrin binding 9.00e-04 1.40e-01 clathrin adaptor activity 1.54e-03 2.10e-01 DNA replication factor A complex 1.55e-03 2.82e-01 cell-cell adhesion via plasma-membrane adhesion molecules 1.58e-03 2.29e-01 phosphatidylinositol-3,4-bisphosphate binding 1.90e-03 3.32e-01 clathrin coat assembly 1.97e-03 3.37e-01 protein ADP-ribosylation 2.00e-03 3.41e-01 ATP generation from poly-ADP-D-ribose 2.14e-03 2.99e-01 phosphatidylinositol-3,5-bisphosphate binding 2.21e-03 3.69e-01 regulation of cysteine-type endopeptidase activity involved in apoptotic process 2.36e-03 3.89e-01 regulation of platelet-derived growth factor receptor signaling pathway 2.76e-03 4.42e-01 regulation of cysteine-type endopeptidase activity 2.92e-03 4.62e-01 regulation of endopeptidase activity 2.99e-03 4.71e-01 regulation of proteolysis 3.27e-03 4.29e-01 protein binding involved in cell-cell adhesion

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.32e-04 1.99e-02 APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS 4.29e-04 4.73e-02 APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS 1.60e-03 1.77e-01 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 2.55e-03 2.30e-01 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 2.76e-03 2.80e-01 APOPTOTIC EXECUTION PHASE 4.38e-03 3.67e-01 APOPTOTIC EXECUTION PHASE 1.26e-02 8.86e-01 APOPTOSIS 1.80e-02 1.00e+00 RESOLUTION OF AP SITES VIA THE MULTIPLE NUCLEOTIDE PATCH REPLACEMENT PATHWAY 1.80e-02 1.00e+00 BASE FREE SUGAR PHOSPHATE REMOVAL VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 1.89e-02 1.00e+00 SIGNAL TRANSDUCTION BY L1 1.92e-02 1.00e+00 GENERIC TRANSCRIPTION PATHWAY 2.02e-02 1.00e+00 APOPTOSIS 2.04e-02 1.00e+00 BASE FREE SUGAR PHOSPHATE REMOVAL VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 2.29e-02 1.00e+00 RESOLUTION OF AP SITES VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 2.29e-02 1.00e+00 BASE EXCISION REPAIR 2.43e-02 1.00e+00 DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY 2.62e-02 1.00e+00 RESOLUTION OF AP SITES VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 2.70e-02 1.00e+00 PRE NOTCH TRANSCRIPTION AND TRANSLATION 2.85e-02 1.00e+00 DEFENSINS 3.07e-02 1.00e+00 REGULATORY RNA PATHWAYS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.02e-03 9.1e-01 abnormal orientation of cochlear hair cell stereociliary bundles 2.14e-03 1.0e+00 decreased heart rate 2.58e-03 1.0e+00 absent heartbeat 3.14e-03 1.0e+00 abnormal brain white matter morphology 5.17e-03 1.0e+00 decreased neuron number 5.63e-03 1.0e+00 abnormal P wave 5.65e-03 1.0e+00 vestibular saccular degeneration 6.12e-03 1.0e+00 abnormal retinal neuronal layer morphology 7.48e-03 1.0e+00 acantholysis 7.49e-03 1.0e+00 thick retinal ganglion layer 8.84e-03 1.0e+00 abnormal cochlea morphology 9.34e-03 1.0e+00 decreased susceptibility to noise-induced hearing loss 9.35e-03 1.0e+00 increased heart rate variability 9.37e-03 1.0e+00 abnormal cochlear hair bundle tip links morphology 9.88e-03 1.0e+00 abnormal hair shaft morphology 1.04e-02 1.0e+00 abnormal motor capabilities/coordination/movement 1.12e-02 1.0e+00 absent mouth 1.13e-02 1.0e+00 abnormal cochlear nerve compound action potential 1.30e-02 1.0e+00 abnormal heartbeat 1.31e-02 1.0e+00 novel environmental response-related retropulsion

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

²FDR corrected p-value (Benjamini-Hochberg)