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Summary of LongSAGE tag cluster data according to breed type |
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| Cluster* |
Tags per cluster† |
Previously characterized genes‡ |
GO categories enriched in the cluster§ |
|
|
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| Tongcheng |
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| 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 |
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| Landrace |
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| 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 |
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*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. | |||
Tang et al. Genome Biology 2007 8:R115 doi:10.1186/gb-2007-8-6-r115 |
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