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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod64

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod64 Module size 46 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 56899 ANKS1B ankyrin repeat and sterile alpha motif domain containing 1B 10513 APPBP2 amyloid beta precursor protein binding protein 2 57524 CASKIN1 CASK interacting protein 1 100360496 CAT family with sequence similarity 9, member B 10695 CNPY3 canopy FGF signaling regulator 3 83992 CTTNBP2 cortactin binding protein 2 151647 FAM19A4 family with sequence similarity 19 member A4, C-C motif chemokine like 55527 FEM1A fem-1 homolog A 56929 FEM1C fem-1 homolog C 2314 FLII FLII, actin remodeling protein 23769 FLRT1 fibronectin leucine rich transmembrane protein 1 23768 FLRT2 fibronectin leucine rich transmembrane protein 2 23767 FLRT3 fibronectin leucine rich transmembrane protein 3 256949 KANK3 KN motif and ankyrin repeat domains 3 163782 KANK4 KN motif and ankyrin repeat domains 4 57631 LRCH2 leucine rich repeats and calponin homology domain containing 2 84859 LRCH3 leucine rich repeats and calponin homology domain containing 3 4034 LRCH4 leucine rich repeats and calponin homology domain containing 4 26018 LRIG1 leucine rich repeats and immunoglobulin like domains 1 9860 LRIG2 leucine rich repeats and immunoglobulin like domains 2 81543 LRRC3 leucine rich repeat containing 3 116135 LRRC3B leucine rich repeat containing 3B 100505591 LRRC3C leucine rich repeat containing 3C 57554 LRRC7 leucine rich repeat containing 7 4794 NFKBIE NFKB inhibitor epsilon 27031 NPHP3 nephrocystin 3 441478 NRARP NOTCH regulated ankyrin repeat protein 60506 NYX nyctalopin 55367 PIDD p53-induced death domain protein 1 4660 PPP1R12B protein phosphatase 1 regulatory subunit 12B 54776 PPP1R12C protein phosphatase 1 regulatory subunit 12C 84988 PPP1R16A protein phosphatase 1 regulatory subunit 16A 26051 PPP1R16B protein phosphatase 1 regulatory subunit 16B 154661 RUNDC3B RUN domain containing 3B 23513 SCRIB scribbled planar cell polarity protein 22941 SHANK2 SH3 and multiple ankyrin repeat domains 2 85358 SHANK3 SH3 and multiple ankyrin repeat domains 3 6585 SLIT1 slit guidance ligand 1 6586 SLIT3 slit guidance ligand 3 9627 SNCAIP synuclein alpha interacting protein 81793 TLR10 toll like receptor 10 51284 TLR7 toll like receptor 7 51311 TLR8 toll like receptor 8 54106 TLR9 toll like receptor 9 8989 TRPA1 transient receptor potential cation channel subfamily A member 1 54902 TTC19 tetratricopeptide repeat domain 19

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 1.44e-01 4.50e-05 GO Roundabout binding molecular_function 1.33e-01 1.80e-08 GO ionotropic glutamate receptor complex cellular_component 1.14e-01 3.20e-07 GO positive regulation of interferon-beta biosynthetic process biological_process 9.43e-02 1.28e-08 Reactome Trafficking and processing of endosomal TLR Immune System 5.89e-02 1.25e-04 GO phosphatase regulator activity molecular_function 5.07e-02 1.09e-06 Reactome TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling Immune System 3.39e-02 1.09e-06 GO positive regulation of interleukin-8 biosynthetic process biological_process 2.00e-02 1.38e-05 GO fibroblast growth factor receptor binding molecular_function 1.89e-02 1.50e-06 GO signaling pattern recognition receptor activity molecular_function 1.48e-02 6.28e-07 GO negative chemotaxis biological_process 1.07e-02 2.94e-04 GO regulation of neuron migration 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 9.00e-09 5.88e-06 negative regulation of JAK-STAT cascade 1.70e-08 7.48e-06 protein kinase inhibitor activity 2.28e-08 9.83e-06 kinase inhibitor activity 1.03e-06 3.26e-04 protein kinase regulator activity 1.46e-06 6.73e-04 positive regulation of interferon-alpha biosynthetic process 1.70e-06 5.17e-04 kinase regulator activity 3.09e-06 1.33e-03 negative chemotaxis 6.32e-06 1.72e-03 ionotropic glutamate receptor binding 7.53e-06 3.00e-03 MyD88-dependent toll-like receptor signaling pathway 8.47e-06 3.34e-03 positive regulation of interferon-beta biosynthetic process 1.26e-05 4.76e-03 regulation of JAK-STAT cascade 1.35e-05 5.06e-03 positive regulation of interferon-gamma biosynthetic process 2.28e-05 5.56e-03 glutamate receptor binding 2.50e-05 6.05e-03 siRNA binding 3.44e-05 8.08e-03 enzyme inhibitor activity 4.40e-05 1.44e-02 toll-like receptor signaling pathway 5.06e-05 1.14e-02 fibroblast growth factor receptor binding 5.29e-05 1.68e-02 toll-like receptor 9 signaling pathway 5.56e-05 1.17e-02 endolysosome membrane 6.50e-05 2.01e-02 positive regulation of interferon-alpha production

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.40e-09 7.82e-07 TRAFFICKING AND PROCESSING OF ENDOSOMAL TLR 1.81e-08 3.86e-06 TOLL RECEPTOR CASCADES 8.59e-08 2.23e-05 TRAFFICKING AND PROCESSING OF ENDOSOMAL TLR 1.10e-07 2.13e-05 TRAF6 MEDIATED IRF7 ACTIVATION IN TLR7 8 OR 9 SIGNALING 1.24e-07 3.17e-05 TOLL RECEPTOR CASCADES 4.96e-07 1.17e-04 TRAF6 MEDIATED IRF7 ACTIVATION IN TLR7 8 OR 9 SIGNALING 2.35e-06 3.85e-04 TRAF6 MEDIATED INDUCTION OF NFKB AND MAP KINASES UPON TLR7 8 OR 9 ACTIVATION 1.11e-05 1.64e-03 INNATE IMMUNE SYSTEM 1.16e-05 2.19e-03 TRAF6 MEDIATED INDUCTION OF NFKB AND MAP KINASES UPON TLR7 8 OR 9 ACTIVATION 2.68e-05 4.74e-03 INNATE IMMUNE SYSTEM 1.61e-03 1.78e-01 NETRIN1 SIGNALING 1.77e-03 1.68e-01 NETRIN1 SIGNALING 8.62e-03 7.11e-01 ACTIVATION OF NF KAPPAB IN B CELLS 1.55e-02 1.00e+00 DOWNSTREAM SIGNALING EVENTS OF B CELL RECEPTOR BCR 1.95e-02 1.00e+00 ACTIVATION OF NF KAPPAB IN B CELLS 2.31e-02 1.00e+00 PURINE CATABOLISM 2.42e-02 1.00e+00 DOWNSTREAM SIGNALING EVENTS OF B CELL RECEPTOR BCR 2.44e-02 1.00e+00 SIGNALING BY EGFR IN CANCER 3.85e-02 1.00e+00 SIGNALING BY EGFR IN CANCER 3.88e-02 1.00e+00 PURINE CATABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.48e-04 5.68e-01 increased aggression towards mice 1.13e-03 9.65e-01 abnormal response to novelty 1.29e-03 1.00e+00 decreased interleukin-12b secretion 1.66e-03 1.00e+00 increased stereotypic behavior 1.86e-03 1.00e+00 herniated abdominal wall 2.34e-03 1.00e+00 abnormal nest building behavior 2.86e-03 1.00e+00 increased grooming behavior 4.00e-03 1.00e+00 decreased tumor necrosis factor secretion 4.14e-03 1.00e+00 reduced long term depression 4.96e-03 1.00e+00 abnormal auditory brainstem response waveform shape 5.64e-03 1.00e+00 abnormal medium spiny neuron morphology 6.01e-03 1.00e+00 abnormal dendritic spine morphology 6.81e-03 1.00e+00 vertebral fusion 7.14e-03 1.00e+00 abnormal vocalization 7.20e-03 1.00e+00 hyporesponsive to tactile stimuli 7.49e-03 1.00e+00 abnormal sleep behavior 1.12e-02 1.00e+00 increased B-2 B cell number 1.12e-02 1.00e+00 photophobia 1.12e-02 1.00e+00 failure of ventral body wall closure 1.15e-02 1.00e+00 increased thigmotaxis

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

²FDR corrected p-value (Benjamini-Hochberg)