Functional annotation clustering for genes highly expressed in the Longissimus muscle of Basque (B, n = 20) pigs.

a<p>Gene ontology identification number.</p>b<p>Name of the ontology.</p>c<p>n_G, number of genes in the category.</p>d<p>Modified Fisher's exact test P value.</p

Differences between Basque (B, n = 20) and Large White (LW, n = 20) breeds for growth, body composition, and Longissimus muscle characteristics.

a<p>Residual Standard Deviation.</p>b<p>P value of breed effect.</p>c<p>Score between 0 to 10.</p>d<p>A significant effect of housing system was found (A: 4.0 and C: 4.4, P = 1.8E-02).</p

Validation of twelve microarray differentially expressed genes by quantitative PCR.

<p>Fold change value is expressed as the expression ratio of Basque (B, n = 20) to Large White (LW, n = 20) samples when genes are highly expressed in Basque pigs and as the negative expression ratio of LW to B samples when genes are highly expressed in LW pigs. Statistical significances are reported below the plot as Benjamini and Hochberg adjusted P value for microarray data and as Student t-test P value for qPCR data (bold case). <i>ADAMTS8</i>, ADAM metallopeptidase with thrombospondin type 1 motif, 8; <i>ANKRD1</i>, ankyrin repeat domain 1; <i>FABP3</i>, Fatty acid-binding protein, heart; <i>FHL3</i>, Four and a half LIM domains 3; <i>FOS</i>, FBJ murine osteosarcoma viral oncogene homolog; <i>GLOD4</i>, glyoxalase domain containing 4; <i>HHATL</i>, hedgehog acyltransferase-like; <i>IGF1</i>, insulin-like growth factor 1; <i>LIPE</i>, lipase, hormone-sensitive; <i>PPARD</i>, peroxisome proliferator-activated receptor delta; <i>SPARC</i>, secreted protein acidic and rich in cysteine; <i>ZNF24</i>, zinc finger protein 24.</p

Functional annotation clustering for genes highly expressed in the Longissimus muscle of Large White (LW, n = 20) pigs.

a<p>Gene ontology identification number.</p>b<p>Name of the ontology.</p>c<p>n_G, number of genes in the category.</p>d<p>modified Fisher's exact test P value.</p

Relevant biological processes significantly enriched in the two lists of differentially expressed genes.

a<p>Gene ontology identification number.</p>b<p>n_G = number of genes in the category.</p>c<p>Modified Fisher's exact test P value.</p

Microarray Biological Process (GO Slim) classification.

<p>Each Biological Process category is represented by a bar. The height of the bar represents the percentage of genes observed in the category. The number of genes per category is indicated upon the bars text.</p

Validation of seven microarray differentially expressed genes between Longissimus (LM) and Semimembranosus (SM) muscles by quantitative RT-PCR.

<p>mRNA level is expressed using arbitrary units. Quantitative RT-PCR expression levels (LM = 8, SM = 8) were normalized to the expression of beta 2 microglobulin (<i>B2M</i>), TATAbox binding protein (<i>TBP</i>) and <i>18S</i> using geNorm algorithm. Microarray adjusted means for LM and SM (LM = 90; SM = 90) were calculated using least square means for the muscle effect. Data are expressed as means±s.d. Statistical significances are reported below the plot as Benjamini and Hochberg adjusted P-value for microarray data and as Student t-test P value for q RT-PCR. Fold change ratio is expressed as the expression ratio of LM to SM when genes are overrepresented in LM and as the expression ratio of SM to LM when genes are overrepresented in SM.</p

Comparison of microarray and qPCR data for eight genes in pigs divergently selected for low or high residual feed intake (RFI).

<p>Transcriptomic differences between the two lines were validated by qPCR at 132 and 74 days of age (onset of the growing period). For values related to microarray, the highest P-value is reported when several probes are differentially expressed for a unique gene (*P < 0.05; **P < 0.01; ***P<0.001). Fold change value is expressed as the expression ratio of low RFI to high RFI samples; ratio was inversed and preceded by a minus sign for value less than 1 (i.e., a ratio of 0.5 is expressed as -2). <i>CD40</i>, tumor necrosis factor receptor superfamily member 5; <i>GPX3</i>, glutathione peroxidase 3; <i>OAZ3</i>, ornithine decarboxylase antizyme 3; <i>DGAT2</i>, diacylglycerol O-acyltransferase 2; <i>NMI</i>, N-myc interactor; <i>TRAF6</i>, TNF receptor-associated factor 6; <i>SLPI</i>, secretory leukocyte peptidase inhibitor; <i>PSEN1</i>, presenilin 1.</p

Relevant biological pathways significantly enriched in clustered differentially expressed genes.

1<p>Differentially expressed genes were clustered using GO BP terms semantic similarity between genes as distance, to group functionally similar genes together.</p>2<p>Cluster enrichment score (ES).</p>3<p>n_G, number of genes in the category.</p>4<p>Benjamini and Hochberg adjusted P value.</p

Primers pairs used in quantitative real-time RT-PCR.

1<p>ADAMTS8, ADAM metallopeptidase with thrombospondin type 1 motif, 8; ALDOA, aldolase A, fructose-bisphosphate; B2M, beta-2-microglobulin; CEBPA, CCAAT/enhancer binding protein (C/EBP), alpha; CPT1B, carnitine palmitoyltransferase 1B (muscle); DGAT2, diacylglycerol O-acyltransferase 2; RYR1, ryanodine receptor 1 (skeletal); TBP1, TATA box binding protein; TGFB1, transforming growth factor, beta 1.</p>2<p>Accession number of the Sus scrofa sequence used to design primers.</p>3<p>Gene used as reference for normalization.</p