Milk yield responses to changes in milking frequency during early lactation are associated with coordinated and persistent changes in mammary gene expression

Wall, Emma H; Bond, Jeffrey P; McFadden, Thomas B

doi:10.1186/1471-2164-14-296

Table 1 Mammary expression of genes regulated by changes in milking frequency in dairy cows during early lactation ¹

From: Milk yield responses to changes in milking frequency during early lactation are associated with coordinated and persistent changes in mammary gene expression

Gene Title	Gene Symbol	Cluster⁴	Fold change²(d21)	P-value (d21)	Fold change (d23)	P-value (d23)	Fold change (d40)	P-value (d40)	Time³(P-value)	Probe ID
Aldehyde dehydrogenase 1 family, member A3	ALDH1A3	1	−1.90	0.003	1.08	0.703	−1.27	0.233	0.016	Bt.8798.1.S1_at
Apolipoprotein E	APOE	1	−1.73	0.024	1.18	0.480	−1.47	0.101	0.037	Bt.5215.1.S1_at
MHC class I heavy chain	BOLA	1	−1.62	0.018	1.24	0.267	−1.11	0.594	0.016	Bt.29824.1.S1_s_at
Chromosome 20 open reading frame 108 ortholog	C13H20ORF108	1	−1.78	0.001	1.18	0.290	−1.57	0.007	0.002	Bt.1858.1.A1_at
Complement component 4 binding protein, alpha	C4BPA	1	−1.75	0.045	1.68	0.061	−1.32	0.308	0.008	Bt.4707.1.A1_at
Chemokine (C-C motif) ligand 2, 11	CCL-2, -11	1	−1.99	0.003	1.12	0.566	−1.33	0.172	0.010	Bt.2408.1.S1_s_at
Complement factor B	CFB	1	−2.46	0.001	1.35	0.226	−1.82	0.021	0.002	Bt.13542.1.S1_at
Complement factor I	CFI	1	−3.26	0.002	1.54	0.204	−2.16	0.029	0.002	Bt.13387.1.S1_at
Chitinase 3-like 1 (cartilage glycoprotein-39)	CHI3L1	1	−3.90	0.009	2.79	0.041	−2.26	0.098	0.002	Bt.5238.1.S1_at
Claudin 4	CLDN4	1	−1.90	< 0.001	1.06	0.679	−1.23	0.165	0.002	Bt.12177.1.S1_at
Clusterin	CLU	1	−2.42	0.004	1.46	0.185	−1.98	0.022	0.004	Bt.12504.1.S1_at
Crystallin, alpha B	CRYAB	1	−1.83	0.001	1.43	0.045	−1.42	0.047	0.001	Bt.222.1.S1_at
Colony stimulating factor 1 receptor	CSF1R	1	−1.83	0.002	1.13	0.484	−1.44	0.048	0.008	Bt.21071.2.A1_at
Cytochrome b-561	CYB561	1	−1.62	0.001	1.29	0.051	−1.32	0.036	< 0.001	Bt.4360.1.S1_at
Cytochrome b reductase 1	CYBRD1	1	−2.06	0.004	1.38	0.163	−2.07	0.003	0.003	Bt.22055.1.S1_at
Cytochrome P450, family 11, subfamily A, polypeptide 1	CYP11A1	1	−1.97	0.007	1.30	0.264	−1.50	0.090	0.008	Bt.7190.1.S1_at
Early growth response 1	EGR1	1	−2.36	< 0.001	1.53	0.055	−1.83	0.009	< 0.001	Bt.22265.1.S1_at
v-erb-b2 homolog 3	ERBB3	1	−1.76	< 0.001	1.33	0.049	−1.54	0.005	< 0.001	Bt.19517.1.S1_at
v-fos FBJ murine osteosarcoma viral oncogene homolog	FOS	1	−2.68	0.001	1.33	0.257	−1.40	0.187	0.002	Bt.2899.1.S2_at
Forkhead box Q1	FOXQ1	1	−2.82	0.004	1.34	0.370	−1.76	0.092	0.008	Bt.15658.1.S1_at
Inositol 1,4,5-triphosphate receptor, type 1	ITPR1	1	−1.80	0.007	1.14	0.511	−1.70	0.014	0.018	Bt.23606.1.S1_at
Jun oncogene	JUN	1	−2.28	0.001	1.23	0.348	−1.11	0.620	0.003	Bt.11159.1.S1_at
V-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	KIT	1	−1.82	0.011	1.19	0.421	−1.56	0.050	0.018	Bt.26445.1.A1_at
Kruppel-like factor 10	KLF10	1	−2.15	0.001	1.11	0.609	−1.40	0.117	0.007	Bt.9527.2.S1_at
Kruppel-like factor 11	KLF11	1	−1.89	0.001	1.08	0.644	−1.42	0.054	0.007	Bt.16916.3.S1_at
Keratin 15	KRT15	1	−1.89	0.006	1.17	0.454	−1.55	0.046	0.013	Bt.22801.1.S1_at
Keratin 7	KRT7	1	−1.84	0.002	1.21	0.278	−1.40	0.066	0.004	Bt.8105.1.S1_at
Keratin 8	KRT8	1	−2.17	0.002	1.32	0.209	−1.51	0.072	0.002	Bt.23608.1.S1_s_at
Lectin, galactoside-binding, soluble	LGALS3	1	−2.12	0.002	1.22	0.361	−1.51	0.063	0.004	Bt.1416.1.S1_at
Hypothetical LOC516522	LOC516522	1	−2.04	0.004	1.20	0.415	−1.95	0.007	0.010	Bt.24918.1.A1_at
Similar to Probable phospholipid-transporting ATPase IIA (ATPase class II type 9A)	LOC516579	1	−1.77	0.003	1.13	0.470	−1.41	0.056	0.009	Bt.21546.1.S1_at
Hypothetical protein LOC785058	LOC785058	1	−1.95	0.007	1.54	0.068	−1.15	0.533	0.002	Bt.9679.1.S1_at
Hypothetical protein LOC786129	LOC786129	1	−1.78	0.005	1.21	0.311	−1.37	0.099	0.007	Bt.685.1.A1_at
Similar to Extracellular proteinase inhibitor	LOC787253	1	−1.68	0.005	1.20	0.277	−1.05	0.750	0.006	Bt.9675.1.S1_at
Leukotriene A4 hydrolase	LTA4H	1	−1.64	0.004	1.32	0.089	−1.30	0.110	0.002	Bt.6143.1.S1_at
Lactotransferrin	LTF	1	−1.74	0.004	1.17	0.361	−1.44	0.045	0.008	Bt.4802.1.S1_at
Hypothetical LOC614805	MGC165862	1	−2.33	0.004	1.38	0.228	−1.65	0.066	0.004	Bt.9774.1.S1_a_at
Melanophilin	MLPH	1	−1.82	0.006	1.24	0.284	−1.35	0.135	0.007	Bt.29245.1.A1_at
AT rich interactive domain 5B	ARID5B	1	−1.68	0.010	1.25	0.242	−1.71	0.008	0.010	Bt.13289.2.S1_at
Plexin domain containing 2	PLXDC2	1	−1.71	0.001	1.22	0.172	−1.35	0.045	0.001	Bt.25703.1.A1_at
Protease, serine, 22	PRSS22	1	−1.92	0.007	1.22	0.369	−1.24	0.326	0.012	Bt.29351.1.A1_at
Protein tyrosine phosphatase, receptor type, D	PTPRD	1	−1.88	0.007	1.12	0.603	−1.33	0.199	0.022	Bt.18753.1.A1_at
Retinol binding protein 1, cellular	RBP1	1	−2.44	0.003	1.29	0.358	−1.70	0.060	0.006	Bt.17810.1.S1_a_at
Regulator of G-protein signaling 2, 24 kDa	RGS2	1	−1.95	0.003	1.14	0.520	−1.37	0.128	0.009	Bt.10855.1.S1_at
S100 calcium binding protein A14	S100A14	1	−1.83	0.004	1.13	0.520	−1.54	0.032	0.012	Bt.21342.1.S1_at
S100 calcium binding protein A2	S100A2	1	−2.11	0.007	1.35	0.246	−1.52	0.108	0.007	Bt.5970.1.S1_a_at
Serum amyloid A 3	SAA3	1	−2.96	0.010	2.53	0.024	−1.56	0.259	0.001	Bt.278.1.S1_at
Scinderin	SCIN	1	−1.72	0.005	1.18	0.340	−1.54	0.022	0.009	Bt.3980.1.S1_at
Shisa homolog 2 (Xenopus laevis)	SHISA2	1	−1.85	0.011	1.19	0.447	−1.61	0.043	0.021	Bt.22389.1.S1_at
Solute carrier family 1, member 1	SLC1A1	1	−1.54	0.010	1.36	0.058	−1.36	0.055	0.003	Bt.23659.1.S1_at
Sortilin 1	SORT1	1	−1.62	0.002	1.25	0.113	−1.19	0.216	0.001	Bt.23586.1.S1_at
Sex determining region Y)-box 4	SOX4	1	−1.89	0.007	1.23	0.342	−1.78	0.013	0.011	Bt.12453.1.A1_at
Sex determining region Y-box 9	SOX9	1	−1.80	0.023	1.16	0.543	−1.84	0.019	0.042	Bt.6983.1.S1_at
Tumor-associated calcium signal transducer 2	TACSTD2	1	−2.19	0.005	1.27	0.351	−1.43	0.166	0.009	Bt.1694.1.S1_at
Transcription factor CP2-like 1	TFCP2L1	1	−1.81	0.004	1.16	0.433	−1.42	0.067	0.009	Bt.28282.1.S1_at
Thrombospondin 1	THBS1	1	−2.11	0.001	1.15	0.467	−1.57	0.023	0.003	Bt.5301.1.S1_at
Zinc finger protein 36	ZNF36	1	−1.67	0.001	1.21	0.158	−1.40	0.017	0.001	Bt.19706.1.S1_at
Transcribed locus	-	1	−1.84	0.012	1.20	0.428	−2.12	0.003	0.020	Bt.18855.1.A1_at
Transcribed locus	-	1	−2.13	0.007	1.37	0.230	−2.07	0.009	0.007	Bt.13764.1.S1_at
Transcribed locus	-	1	−1.56	0.003	1.41	0.016	−1.45	0.010	< 0.001	Bt.25328.1.A1_at
Transcribed locus	-	1	−1.68	0.011	1.21	0.316	−1.48	0.047	0.013	Bt.24919.1.S1_at
IQ motif containing GTPase activating protein 1	IQGAP1	2	−1.58	0.015	1.46	0.042	1.22	0.267	0.003	Bt.21982.1.S1_a_at
RNA binding motif protein 5	RBM5	2	−1.68	0.005	1.46	0.032	1.17	0.358	0.001	Bt.27798.1.A1_at
S100 calcium binding protein A12	S100A12	2	−1.58	0.077	1.32	0.268	1.00	0.986	0.046	Bt.357.1.S1_at
ATPase type 13A4	ATP13A4	3	1.78	0.005	−1.13	0.517	1.04	0.835	0.015	Bt.25459.1.A1_at
Frizzled family receptor 5	FZD5	3	1.95	0.001	−1.06	0.769	1.20	0.335	0.011	Bt.16100.2.S1_at
Hypothetical protein LOC540918	LOC540918	3	1.89	0.001	−1.14	0.435	1.21	0.246	0.003	Bt.12714.1.A1_at
Lipin1	LPIN1	3	1.90	0.004	−1.09	0.661	1.18	0.424	0.017	Bt.6642.2.S1_at
Myosin binding protein C, slow type	MYBPC1	3	1.78	0.006	−1.14	0.493	1.25	0.250	0.015	Bt.23229.1.S1_at
Nebulin	NEB	3	1.75	0.002	−1.21	0.238	1.28	0.134	0.003	Bt.14153.1.S1_at
Oxidative stress induced growth inhibitor family member 2	OSGIN2	3	1.73	0.001	−1.18	0.265	1.04	0.771	0.002	Bt.21696.1.S1_at
Transcribed locus	-	3	1.82	0.009	−1.29	0.232	1.03	0.879	0.008	Bt.21137.2.S1_at
Low density lipoprotein related protein 2	LRP2	4	1.94	< 0.001	−1.13	0.315	−1.01	0.950	< 0.001	Bt.8371.1.S1_at
Myostatin	MSTN	4	1.78	< 0.001	−1.19	0.188	−1.28	0.067	< 0.001	Bt.8967.1.S1_at
Solute carrier family 34	SLC34A2	4	1.74	0.007	−1.18	0.389	−1.02	0.914	0.013	Bt.21137.1.S1_at

¹Cows (n = 6) were assigned to twice daily milking (2×) of the left udder half and four times daily milking (4×) of the right udder half during d 1 to 21 of lactation. Mammary biopsies from both udder halves were obtained on d 21, 23, and 40 of lactation. Differential gene expression was detected using Affymetrix GeneChip® Bovine Genome Arrays.
²Signed fold change (4× vs. 2× udder halves).
³Time = change in differential gene expression between 2× and 4× udder halves on day 21 vs. that on day 23 (magnitude of difference ≥ 2; P ≤ 0.05).
⁴Genes were grouped into four clusters based on the temporal pattern of differential expression.
Genes in bold were consistently differentially expressed in a previous independent microarray experiment [15].

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