The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

Lencer, Ezra S.; Warren, Wesley C.; Harrison, Richard; McCune, Amy R.

doi:10.1186/s12864-017-3810-7

Table 1 Enrichment (GSEA) of top Hallmark Gene Sets along principal component axes for each stage

From: The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

48 Hours Post Fertilization		96 Hours Post Fertilization		8 Days Post Fertilization		15 Days Post Fertilization
PC1 (Separates Marine From Inland Taxa)		PC1 (Separates Marine From Inland Taxa)		PC1 (Separates Scale-Biter From Taxa)		PC2 (Separates Marine From Inland Taxa)
Name	NES	Name	NES	Name	NES	Name	NES
Positive Loadings:		Positive Loadings:		Positive Loadings:		Positive Loadings:
E2F Targets	2.84	Interferon Gamma Resp.	2.81	Uv Response Dn	2.53	Myogenesis	2.99
G2M Checkpoint	2.73	Interferon Alpha Response	2.14	Il2 Stat5 Signaling	2.36	Il2 Stat5 Signaling	2.88
Mitotic Spindle	2.17	Xenobiotic Metabolism	2.14	Tnfa Signaling Via Nfkb	2.35	Uv Response Dn	2.86
Protein Secretion	2.14	Bile Acid Metabolism	1.98	Kras Signaling Dn	2.29	Inflammatory Response	2.64
Myc Targets V1	1.86	Protein Secretion	1.82	Allograft Rejection	2.18	Allograft Rejection	2.57
Dna Repair	1.74	Oxidative Phosphorylation	1.80	P53 Pathway	2.10	Kras Signaling Dn	2.54
Xenobiotic Metabolism	1.54	E2F Targets	1.73	Inflammatory Response	1.99	Hedgehog Signaling	2.05
Interferon Alpha Response	1.51	Glycolysis	1.66	Apical Junction	1.94	Apical Junction	2.04
Estrogen Response Late	1.50	Il6 Jak Stat3 Signaling	1.66	Kras Signaling Up	1.83	Coagulation	2.01
Negative Loadings:		Negative Loadings:		Negative Loadings:		Negative Loadings:
Epith. Mesench. Trans.	−3.07	Tnfa Signaling Via Nfkb	−1.81	E2F Targets	−8.13	Myc Targets V1	−5.97
Coagulation	−2.12	Myc Targets V1	−1.74	G2M Checkpoint	−6.50	E2F Targets	−5.78
Kras Signaling Dn	−1.80	Epith. Mesench. Trans.	−1.70	Myc Targets V1	−5.56	G2M Checkpoint	−4.91
Oxidative Phosphorylation	−1.63	Apical Junction	−1.63	mTORc1 Signaling	−4.51	Oxidative Phosph.	−4.38
Peroxisome	−1.61	Kras Signaling Up	−1.62	Oxidative Phosph.	−3.06	Myc Targets V2	−4.03
Inflammatory Response	−1.53	Androgen Response	−1.48	Dna Repair	−2.87	mTORc1 Signaling	−3.59
Il2 Stat5 Signaling	−1.29	Kras Signaling Dn	−1.29	Myc Targets V2	−2.84	Dna Repair	−3.55
Myc Targets V2	−1.25	Uv Response Dn	−1.23	Unfolded Protein Resp.	−2.54	Fatty Acid Metabolism	−2.91
Pancreas Beta Cells	−1.25	Notch Signaling	−1.19	Mitotic Spindle	−2.50	Unfolded Protein Resp.	-2.44
PC2 (Separates Taxa By Morphology)		PC2 (Separates Taxa By Morphology)		PC2 (Separates Marine From Inland Taxa)		PC3 (Separates Scale-Biter From Taxa)
Name	NES	Name	NES	Name	NES	Name	NES
Positive Loadings:		Positive Loadings:		Positive Loadings:		Positive Loadings:
Myc Targets V1	3.98	Myogenesis	2.92	E2F Targets	6.93	Kras Signaling Dn	2.86
Oxidative Phosph.	3.10	Kras Signaling Up	2.27	Myc Targets V1	5.41	Uv Response Dn	2.64
Dna Repair	2.83	Interferon Gamma Resp.	2.21	G2M Checkpoint	4.95	Myogenesis	2.60
E2F Targets	2.50	Coagulation	1.90	Myc Targets V2	3.80	Epith. Mesench. Trans.	2.55
Myc Targets V2	2.48	Protein Secretion	1.83	Dna Repair	3.07	Tgf Beta Signaling	2.11
G2M Checkpoint	2.03	Apical Junction	1.82	mTORc1 Signaling	3.04	Hedgehog Signaling	2.06
Mitotic Spindle	1.87	Uv Response Dn	1.79	Unfolded Protein Response	2.86	Apical Junction	2.00
Bile Acid Metabolism	1.66	Epith. Mesench. Trans.	1.79	Oxidative Phosphorylation	1.96	Bile Acid Metabolism	1.96
mTORc1 Signaling	1.27	Kras Signaling Dn	1.74	Pancreas Beta Cells	1.74	Wnt B-Catenin Signaling	1.91
Negative Loadings:		Negative Loadings:		Negative Loadings:		Negative Loadings:
Hypoxia	−2.76	G2M Checkpoint	−3.33	Myogenesis	−3.90	E2F Targets	−5.20
Epith. Mesench. Trans.	−2.69	Myc Targets V1	−2.96	Tnfa Signaling Via Nfkb	−3.54	mTORc1 Signaling	−5.05
Estrogen Response Early	−2.28	E2F Targets	−2.75	Hypoxia	−3.07	Myc Targets V1	−4.85
Pi3K/Akt/mTOR Sig.	−1.87	Oxidative Phosphorylation	−1.99	Interferon Gamma Resp.	−2.86	G2M Checkpoint	−4.03
Protein Secretion	−1.76	Myc Targets V2	−1.95	Il6 Jak Stat3 Signaling	−2.82	Myc Targets V2	−3.76
Tnfa Signaling Via Nfkb	−1.73	Dna Repair	−1.85	Epith. Mesench. Trans.	−2.74	Dna Repair	-3.50
P53 Pathway	−1.63	Wnt B-Catenin Signaling	−1.72	Uv Response Dn	−2.66	Unfolded Protein Resp.	−2.77
Kras Signaling Up	−1.60	Unfolded Protein Response	−1.68	Kras Signaling Up	−2.62	Oxidative Phosph.	−2.29
Myogenesis	−1.57	mTORc1 Signaling	−1.52	P53 Pathway	−2.57	Cholesterol Homeostasis	−2.19

Shown are the top 9 hallmark pathways for each PC axis at each stage. Gene sets in bold are significant at FDR ≤ 0.25. NES normalized enrichment

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ISSN: 1471-2164

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