CliPPER is an empirical method based on Gaussian graphical models that (i) selects pathways with covariance matrices or means significantly different between two experimental conditions; (ii) on such pathways, identifies the portions of the pathways, called signal paths, mostly associated to the phenotype. The significant pathways reported have both tests significant at alpha level <= 0.05.

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Pathway	alphaMean	alphaVar
BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members	0.02	0.02
Apoptosis	0.05	0.01
G1 Phase	0.01	0.05
Cyclin D associated events in G1	0.02	0.05
CDT1 association with the CDC6:ORC:origin complex	0.09	0.04
HDL-mediated lipid transport	0.03	0.1
Ubiquitin-dependent degradation of Cyclin D	0.15	0.0
Vitamin D (calciferol) metabolism	0.15	0.0
Regulation of APC/C activators between G1/S and early anaphase	0.16	0.01
Assembly of the pre-replicative complex	0.13	0.05
Regulation of activated PAK-2p34 by proteasome mediated degradation	0.18	0.0
Ubiquitin-dependent degradation of Cyclin D1	0.15	0.03
Signal transduction by L1	0.16	0.03
Negative regulators of RIG-I/MDA5 signaling	0.18	0.02
Interaction between L1 and Ankyrins	0.15	0.05
Regulation of mitotic cell cycle	0.22	0.0
Xenobiotics	0.23	0.01
APC/C-mediated degradation of cell cycle proteins	0.26	0.0
Mitotic G1-G1/S phases	0.26	0.01
Oxygen-dependent Proline Hydroxylation of Hypoxia-inducible Factor Alpha	0.28	0.01
Processing of Capped Intronless Pre-mRNA	0.26	0.03
RIP-mediated NFkB activation via DAI	0.28	0.04
Cytosolic sensors of pathogen-associated DNA	0.29	0.04
Tat-mediated elongation of the HIV-1 transcript	0.31	0.04
Degradation of beta-catenin by the destruction complex	0.33	0.02
Cellular response to hypoxia	0.33	0.03
RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways	0.32	0.05
Voltage gated Potassium channels	0.36	0.01
Formation of RNA Pol II elongation complex	0.39	0.01
HIV-1 Transcription Elongation	0.43	0.0
SLBP independent Processing of Histone Pre-mRNAs	0.43	0.0
G1/S Transition	0.44	0.0
Formation of HIV-1 elongation complex containing HIV-1 Tat	0.43	0.03
Toll Receptor Cascades	0.49	0.0
Regulation of Hypoxia-inducible Factor (HIF) by Oxygen	0.49	0.01
Cellular responses to stress	0.48	0.04
Receptor-ligand binding initiates the second proteolytic cleavage of Notch receptor	0.51	0.04
Pre-NOTCH Processing in the Endoplasmic Reticulum	0.53	0.05
U12 Dependent Splicing	0.58	0.02
Transport to the Golgi and subsequent modification	0.63	0.0
Activated TLR4 signalling	0.66	0.01
EGFR interacts with phospholipase C-gamma	0.66	0.01
Signaling by NOTCH1	0.66	0.02
Toll Like Receptor 4 (TLR4) Cascade	0.67	0.01
PLCG1 events in ERBB2 signaling	0.7	0.01
DAG and IP3 signaling	0.72	0.01
NICD traffics to nucleus	0.75	0.0
Calmodulin induced events	0.75	0.01
Ca-dependent events	0.77	0.01
Phospholipase C-mediated cascade	0.75	0.03
PKA-mediated phosphorylation of CREB	0.75	0.03
CaM pathway	0.78	0.01
mRNA Decay by 3' to 5' Exoribonuclease	0.76	0.03
PLC-gamma1 signalling	0.77	0.02
Notch-HLH transcription pathway	0.78	0.02
Eukaryotic Translation Termination	0.79	0.02
Asparagine N-linked glycosylation	0.8	0.02
RNA Pol II CTD phosphorylation and interaction with CE	0.77	0.05
GTP hydrolysis and joining of the 60S ribosomal subunit	0.79	0.04
G-protein mediated events	0.79	0.05
PKA activation	0.83	0.02
PLC beta mediated events	0.84	0.01
CREB phosphorylation through the activation of CaMKK	0.83	0.04
Formation of a pool of free 40S subunits	0.82	0.05
Spry regulation of FGF signaling	0.86	0.01
ERKs are inactivated	0.84	0.05
mRNA Processing	0.87	0.02
SRP-dependent cotranslational protein targeting to membrane	0.88	0.02
Translation	0.9	0.0
Nonsense-Mediated Decay	0.91	0.0
Cap-dependent Translation Initiation	0.9	0.02
Eukaryotic Translation Initiation	0.88	0.04
Nonsense Mediated Decay Enhanced by the Exon Junction Complex	0.91	0.01
Nonsense Mediated Decay Independent of the Exon Junction Complex	0.88	0.05
mRNA Splicing	0.92	0.02
Ionotropic activity of Kainate Receptors	0.95	0.01
Activation of Ca-permeable Kainate Receptor	0.95	0.02
pre-mRNA splicing	0.93	0.04
Cam-PDE 1 activation	0.98	0.01
RNA Polymerase I Transcription Termination	0.99	0.01