Table 4.

Summary of LongSAGE tag cluster data according to breed type

Cluster*	Tags per cluster†	Previously characterized genes‡	GO categories enriched in the cluster§
Tongcheng
1	191	APOBEC2, BIN1, BTBD1, CACNB1, MYBPC1, MYL1, MYOZ1, RRAS, RTN4, SH3BGR, SLN, TCAP, TMOD1, TNNC2, TNNT3, TPM1	Muscle development (0.0007806)
2	245	ACTN2, AMPD1, ATP2A1, CKM, DES, ENO3, MYH2, RYR1, TMOD4, TPM2, GAPDH, IGF2	Carbohydrate metabolism (0.001492) Mitochondrion (0.016297)
3	204	LASS2	Signal transduction (0.008368)
4	160	SPARC, HSPB2, ATF4, MYL2	Tricarboxylic acid cycle (0.021523489)
5	152	MYH3, S100A11	Ribosomal (1.25E-06)
6	77
7	218	PSMD2, RTN2, SERF1A, THBS4, TIMM13, TNNC1, TNNI1, TNNT1, FAU, HSPA8, FHL1C, HDAC5, MYOT	Obsolete molecular function (0.048234)
8	153	DGKZ, GNB2L1	Binding (0.023903)
Total	1,400
Landrace
1	158	APOBEC2, CFL2, HSPB2, ITGB1, MYH3, PGM5, RTN4, TNNT1, TPM2, FHL1C	Muscle development (0.003181)
2	94	SPARC, TIMM13	Mitochondrion (0.002539)
3	126	AMPD1, CKM, DES, MYBPC1, MYL1, MYOZ1, PFDN5, RYR1, SLN, TNNT3, MYL2	Muscle contraction (0.035242)
4	160	LGALS1, SERF1A1, FAU, HSPA8	Ribosomal (4.83E-07)
5	84		Cytoskeleton organization and biogenesis (0.012664)
6	301	GSN, TPM3, TPM4, TRIO, S100A11, NACA, SUMO2	Cell cycle (0.002587)
7	95	CACNB1, MYLPF, TMOD1, TNNI1, IGF2	Development (0.014224)
8	183	ACTN2, ATP2A1, BIN1, CCNG1, ENO3, MYH2, RTN2, SH3BGR, TCAP, TPM1, GAPDH, SDHD, HDAC5	Protein complex assembly (0.035886)
Total	1,201

*The expression patterns in each cluster for Tongcheng and Landrace pigs are shown as (A) and (B) in Additional data file 6, respectively. ^†Tags in cluster value corresponds to the number of LongSAGE tags in each cluster. ^‡Selected genes previously detected during myogenesis are indicated (references for these are given in Additional data file 7). ^§All significant (p < 0.05) GO categories over-represented in individual clusters were determined by EASE scores [68]; raw EASE scores (Jackknife one-sided Fisher exact p values) for the categories in question are given in parentheses.