Table 2 Gene ontology terms and KEGG pathways determined by pairwise comparisons of embryonic lineages

 EB ICM

Endodermal cell fate specification (7.07e−04)

IL-6-mediated signalling pathway (1.05e−03)

Positive regulation of canonical Wnt sig. path. (1.28e−03)

Positive regulation of JAK-STAT cascade (2.37e−03)

Stem cell population maintenance (4.00e−03)

Signalling pathways regulating pluripotency of stem cells (2.43e−06)

Calcium signalling pathway (8.48e−06)

Cell adhesion molecules (CAMs) (3.53e−04)

PI3K-Akt signalling pathway (5.57e−04)

 EB TE

Regulation of establishment of cell polarity (5.00e−04)

Positive regulation of cell migration (7.13e−04)

Cell proliferation (2.01e−03)

Positive regulation of cell proliferation (3.71e−03)

Positive regulation of JNK cascade (4.11e−03)

PI3K-Akt signalling pathway (1.23e−02)

Phagosome (1.31e−02)

Jak-STAT signalling pathway (3.17e−02)

Lysosome (4.56e−02)

Cell cycle (8.03e−02)

 LB EPI

Negative regulation of transcription from RNA polymerase II promoter (3.92e−05)

Histone H4-K5 and H4-K8 acetylation (1.69e−03)

Regulation of DNA methylation (1.10e−02)

C-5 methylation of cytosine (2.50e−02)

Chromatin silencing (4.13e−02)

MAPK signalling pathway (5.21e−03)

Neuroactive ligand-receptor interaction (2.55e−02)

Signalling pathways regulating pluripotency of stem cells (3.20e−02)

ErbB signalling pathway (3.66e−02)

Adherens junction (3.75e−02)

 LB HYPO

Transmembrane transport (4.11e−05)

Response to glucose (1.35e−04)

Cholesterol efflux (1.63e−04)

Endodermal cell differentiation (1.81e−03)

Triglyceride homoeostasis (2.12e−03)

PI3K-Akt signalling pathway (4.87e−06)

ECM–receptor interaction (6.09e−06)

Cell adhesion molecules (CAMs) (5.98e−05)

Focal adhesion (2.16e−04)

PPAR signalling pathway (3.87e−04)

 Sph EPI

Axon guidance (1.03e−04)

Regulation of neuron projection development (1.99e−04)

Glycogen catabolic process (3.50e−03)

Embryo implantation (7.88e−03)

Regulation of stem cell division (1.17e−02)

Stem cell population maintenance (1.25e−02)

PPAR signalling pathway (3.72e−22)

HIF-1 signalling pathway (1.54e−11)

Tight junction (3.69e−07)

Signalling pathways regulating pluripotency of stem cells (6.67e−07)

 Sph HYPO

Endodermal cell differentiation (8.04e−05)

Endoderm development (1.74e−04)

Lipid transport (2.54e−04)

Response to glucose (2.84e−04)

Cell fate commitment (5.31e−04)

ECM–receptor interaction (1.20e−04)

TGF-beta signalling pathway (1.77e−04)

Cytokine–cytokine receptor interaction (1.18e−03)

PPAR signalling pathway (2.81e−03)

Cell adhesion molecules (CAMs) (3.93e−03)