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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod4

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod4 Module size 44 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 312312 AIG1 GTPase, IMAP family member 1 80832 APOL4 apolipoprotein L4 79908 BTNL8 butyrophilin like 8 118611 C10orf90 chromosome 10 open reading frame 90 79794 C12orf49 chromosome 12 open reading frame 49 55908 C19orf80 angiopoietin like 8 84417 C2orf40 chromosome 2 open reading frame 40 29903 CCDC106 coiled-coil domain containing 106 92749 CCDC164 dynein regulatory complex subunit 1 11126 CD160 CD160 molecule 100131439 CD300LD CD300 molecule like family member d 163732 CITED4 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4 8857 FCGBP Fc fragment of IgG binding protein 2622 GAS8 growth arrest specific 8 200504 GKN2 gastrokine 2 92344 GORAB golgin, RAB6 interacting 57585 HN1L cramped chromatin regulator homolog 1 83982 IFI27L2 interferon alpha inducible protein 27 like 2 57582 KCNT1 potassium sodium-activated channel subfamily T member 1 284252 KCTD1 potassium channel tetramerization domain containing 1 79047 KCTD15 potassium channel tetramerization domain containing 15 84960 KIAA1984 coiled-coil domain containing 183 753 LDLRAD4 low density lipoprotein receptor class A domain containing 4 84695 LOXL3 lysyl oxidase like 3 4193 MDM2 MDM2 proto-oncogene 4194 MDM4 MDM4, p53 regulator 27085 MTBP MDM2 binding protein 64065 PERP PERP, TP53 apoptosis effector 10848 PPP1R13L protein phosphatase 1 regulatory subunit 13 like 2834 PRLHR prolactin releasing hormone receptor 149628 PYHIN1 pyrin and HIN domain family member 1 25898 RCHY1 ring finger and CHY zinc finger domain containing 1 51246 SHISA5 shisa family member 5 10572 SIVA1 SIVA1 apoptosis inducing factor 7020 TFAP2A transcription factor AP-2 alpha 7021 TFAP2B transcription factor AP-2 beta 7022 TFAP2C transcription factor AP-2 gamma 83741 TFAP2D transcription factor AP-2 delta 339488 TFAP2E transcription factor AP-2 epsilon 64418 TMEM168 transmembrane protein 168 7157 TP53 tumor protein p53 94241 TP53INP1 tumor protein p53 inducible nuclear protein 1 8626 TP63 tumor protein p63 7161 TP73 tumor protein p73

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 4.06e-01 1.14e-17 Reactome Negative regulation of activity of TFAP2 (AP-2) family transcription factors Gene expression (Transcription) 1.84e-01 2.51e-14 Reactome Activation of the TFAP2 (AP-2) family of transcription factors Gene expression (Transcription) 8.24e-02 1.60e-08 Reactome Regulation of TP53 Activity through Association with Co-factors Gene expression (Transcription) 6.88e-02 2.18e-08 Reactome TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain Gene expression (Transcription) 4.83e-02 7.04e-07 Reactome Activation of PUMA and translocation to mitochondria Programmed Cell Death 3.93e-02 1.84e-06 Reactome TP53 Regulates Transcription of Caspase Activators and Caspases Gene expression (Transcription) 1.04e-02 7.69e-08 Reactome TP53 Regulates Transcription of Genes Involved in Cytochrome C Release Gene expression (Transcription) 9.93e-03 8.01e-06 Reactome Regulation of TP53 Activity through Methylation Gene expression (Transcription) 8.75e-04 2.98e-10 GO regulation of signal transduction by p53 class mediator 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 3.23e-07 1.68e-04 signal transduction by p53 class mediator 4.89e-07 2.46e-04 regulation of signal transduction by p53 class mediator 1.61e-06 7.36e-04 intrinsic apoptotic signaling pathway by p53 class mediator 2.34e-06 6.93e-04 p53 binding 4.67e-06 1.94e-03 cellular response to UV 5.34e-06 2.20e-03 intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator 7.74e-06 3.08e-03 regulation of G1/S transition of mitotic cell cycle 7.98e-06 3.16e-03 mitotic G1 DNA damage checkpoint 7.98e-06 3.16e-03 mitotic G1/S transition checkpoint 8.81e-06 3.45e-03 G1 DNA damage checkpoint 1.02e-05 3.94e-03 cellular response to light stimulus 1.17e-05 4.46e-03 regulation of cell cycle G1/S phase transition 1.92e-05 6.93e-03 mitotic DNA damage checkpoint 1.93e-05 6.96e-03 DNA damage response, signal transduction by p53 class mediator 1.98e-05 7.11e-03 negative regulation of G1/S transition of mitotic cell cycle 2.21e-05 7.84e-03 negative regulation of cell cycle G1/S phase transition 2.51e-05 8.77e-03 mitotic DNA integrity checkpoint 3.81e-05 1.27e-02 signal transduction in response to DNA damage 4.23e-05 1.39e-02 DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator 4.29e-05 1.41e-02 DNA damage response, signal transduction resulting in transcription

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.29e-03 2.87e-01 P53 DEPENDENT G1 DNA DAMAGE RESPONSE 1.17e-02 8.35e-01 CELL CYCLE CHECKPOINTS 1.26e-02 9.56e-01 P53 DEPENDENT G1 DNA DAMAGE RESPONSE 1.62e-02 1.00e+00 ACTIVATION OF BH3 ONLY PROTEINS 2.15e-02 1.00e+00 AKT PHOSPHORYLATES TARGETS IN THE CYTOSOL 2.15e-02 1.00e+00 PRE NOTCH TRANSCRIPTION AND TRANSLATION 2.70e-02 1.00e+00 INTRINSIC PATHWAY FOR APOPTOSIS 3.00e-02 1.00e+00 CELL CYCLE CHECKPOINTS 3.38e-02 1.00e+00 TRAFFICKING OF AMPA RECEPTORS 3.57e-02 1.00e+00 PRE NOTCH EXPRESSION AND PROCESSING 3.71e-02 1.00e+00 ACTIVATION OF BH3 ONLY PROTEINS 4.04e-02 1.00e+00 AKT PHOSPHORYLATES TARGETS IN THE CYTOSOL 4.27e-02 1.00e+00 PRE NOTCH TRANSCRIPTION AND TRANSLATION 4.77e-02 1.00e+00 PIP3 ACTIVATES AKT SIGNALING 4.87e-02 1.00e+00 TRAFFICKING OF AMPA RECEPTORS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.33e-07 5.56e-03 decreased thymocyte apoptosis 3.52e-06 2.24e-02 decreased mortality induced by ionizing radiation 1.12e-05 5.09e-02 decreased cellular sensitivity to ionizing radiation 1.51e-05 6.24e-02 decreased cellular sensitivity to gamma-irradiation 2.49e-05 9.06e-02 increased foot pad pigmentation 4.66e-05 1.36e-01 increased mortality induced by ionizing radiation 8.89e-05 2.10e-01 increased lung adenoma incidence 3.60e-04 5.00e-01 abnormal cell cycle 6.71e-04 7.20e-01 decreased cellular sensitivity to ultraviolet irradiation 7.24e-04 7.53e-01 decreased apoptosis 8.45e-04 8.19e-01 increased tumor incidence 1.04e-03 9.21e-01 absent eyelids 1.06e-03 9.29e-01 abnormal chromosome number 1.34e-03 1.00e+00 absent radius 1.38e-03 1.00e+00 decreased cell proliferation 1.49e-03 1.00e+00 decreased keratinocyte proliferation 2.09e-03 1.00e+00 polyploidy 2.12e-03 1.00e+00 increased T cell derived lymphoma incidence 2.30e-03 1.00e+00 abnormal dorsal-ventral axis patterning 2.88e-03 1.00e+00 abnormal ventral body wall morphology

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

²FDR corrected p-value (Benjamini-Hochberg)