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Table 5 RIF prediction for regulatory factors in the whole dataset of DE genes

From: Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics

Probe set Gene symbol Gene RIF1 z- score§ RIF2 z- scoreλ
Ssc.10025.3.S1_at CEBPD CCAAT/enhancer binding protein (C/EBP). delta -3.152 -0.017
Ssc.1012.1.S1_at ZNF277 zinc finger protein 277 -1.251 2.751
Ssc.10128.1.A1_at SIX4 SIX homeobox 4 -2.986 3.127
Ssc.13567.1.A1_at ZHX2 zinc fingers and homeoboxes 2 -0.921 3.454
Ssc.14573.1.S1_at EYA2 Eyes absent homolog 2 -2.907 3.048
Ssc.16976.1.S1_at SREBF2 Sterol regulatory element binding transcription factor 2 -0.970 2.533
Ssc.19163.1.S1_at MXI1 MAX interactor 1. dimerization protein -1.860 3.443
Ssc.19313.1.A1_at MAX MYC associated factor X -3.270 -1.671
Ssc.19537.1.S1_at IRF2 Interferon regulatory factor 2 -2.701 -0.615
Ssc.2001.1.A1_at LHX6 LIM homeobox 6 -1.383 -2.847
Ssc.21096.1.S1_at PAX2 Paired box 2 -0.895 2.378
Ssc.22470.1.S1_at PER3 Period circadian clock 3 -2.258 0.824
Ssc.23498.1.S1_s_at MSTN Myostatin -1.930 2.582
Ssc.24606.1.A1_a_at PPARGC1B Peroxisome proliferator-activated receptor gamma coactivator 1 beta -2.896 0.167
Ssc.26039.1.S1_at RORA RAR-related orphan receptor A -3.597 1.736
Ssc.2719.1.A1_at MTA3 Metastasis associated 1 family, member 3 -1.805 -2.555
Ssc.27410.1.S1_at MYCN v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog -2.823 -0.783
Ssc.27576.1.S1_at MN1 Meningioma (disrupted in balanced translocation) 1 -2.263 -0.086
Ssc.27622.1.S1_at KLF11 Kruppel-like factor 11 -3.789 2.701
Ssc.27964.2.S1_at GATA3 GATA binding protein 3 0.063 -2.061
Ssc.29855.1.A1_at CDCA7 Cell division cycle associated 7 -2.346 0.220
Ssc.30288.1.A1_at GRHL3 Grainyhead-like 3 (Drosophila) 0.489 -2.038
Ssc.30799.1.A1_at DACH1 Dachshund family transcription factor 1 0.772 -2.329
Ssc.3355.1.S1_at HDAC1 Histone deacetylase 1 0.747 -1.971
Ssc.4212.1.A1_at ELK3 ELK3, ETS-domain protein (SRF accessory protein 2) -2.349 -1.032
Ssc.6697.1.S1_at SOX4 SRY (sex determining region Y)-box 4 -3.143 -0.718
Ssc.8529.1.A1_at ZFP36L1 ZFP36 ring finger protein-like 1 -3.282 1.299
Ssc.9136.1.S1_at CCRN4L CCR4 carbon catabolite repression 4-like (S. cerevisiae) -1.056 -2.354
Ssc.9298.1.A1_at IRX3 Iroquois homeobox 3 -2.538 -0.692
  1. §Bootstrap 99% and 95% confidence intervals for RIF1 z-scores: -3.288/2.754 and -2.155/1.898, respectively.
  2. λBootstrap 99% and 95% confidence intervals for RIF2 z-scores: -2.594/3.007 and -1.966/2.030, respectively.