The comparison of predicted (dotted lines) and experimental values (solid lines) of phi and psi angles for three typical alpha-, beta-, and alpha/beta-proteins.

<p>Secondary structures of the proteins are signified at the lower part of each box, with coil, beta-strand, and alpha-helix residues represented by thin lines, thick lines, and thick curves, respectively. (A) phi angle for 1n7sD; (B) psi angle for 1n7sD; (C) phi angle for 1k5nB; (D) psi angle for 1k5nB; (E) phi angle for 1lj9B; (F) psi angle for 1lj9B.</p

Ramachandran plot and histograms of phi and psi angles calculated from residues in 500 non-homologous training proteins.

<p>(A) Ramachandran plot; (B) histogram of phi angles; (C) histogram of psi angles. Alpha-helix, beta-strand and polyproline-II are represented by “α”, “β” and “P” respectively.</p

Comparison of ANGLOR with random predictor in different environments.

1<p>SS: residues in different secondary structure</p>2<p>SA: residues of different solvent accessibility</p>3<p>AA: 20 amino acid types</p>4<p>MAE±standard error of mean</p

Butyrate induces significant biological effects in cultured MDBK cells.

<p>a): normal cells; b): cells treated with10 mM butyrate for 24 hrs, showing morphological changes including large vacuoles, ragged membranes, lack of distinct intracellular organelles, and increasing spaces between cells. Insert in a) comparison of histone H3 acetylation of normal cells (1) and histone acetylation in butyrate-treated cells (2). c and d: Cell population profiles determined by flow cytometry. c); normal cells and d) cells treated with butyrate. Inserts: BrdU labeling show butyrate blocked the DNA synthesis after 24 hr treatment. Cells were first pulse labeled with BrdU for 30 min. Collected cells were first stained with diluted fluorescent (Fluorescent isothiocyanate, FITC) anti-BrdU antibody and then stained with DNA marker (7-ADD). The fluorescent signal generated by FITC was acquired in a logarithmic mode, and fluorescent signal from the DNA-content marker 7-ADD was normally acquired in the linear signal amplification mode. Cells were separated into three clusters by double staining analysis. Butyrate treatment eliminates cells in S phase (in rectangle box).</p

The biological relevant pathways: Cell cycle regulation by BTG proteins.

<p>The dataset was analyzed by the Ingenuity Pathways Analysis software (Ingenuity® Systems, <a href="http://www.ingenuity.com" target="_blank">www.ingenuity.com</a>). The color indicates the expression level of the genes (red indicating up-regulated genes and green indicating down-regulated genes).</p

Global Canonical Pathway analysis: Comparison of three datasets

<p>(<b>up-, down-regulated gene datasets, and a combined dataset.</b> Datasets were analyzed by the Ingenuity Pathways Analysis software (Ingenuity® Systems, <a href="http://www.ingenuity.com" target="_blank">www.ingenuity.com</a>). The significance is expressed as a <i>p</i>-value, which is calculated using the <b>right-tailed Fisher's Exact Test</b>.</p

Butyrate treatment induces changes in major GO processing.

<p>Butyrate treatment induces changes in major GO processing.</p

Butyrate-induced disruption in non-coding RNA expression.

*<p>No detectable in control samples.</p

Summary of RNA-Seq coverage data.

<p>BT; butyrate treated; C: Control.</p

The biological relevant pathways: Cell Cycle Control of Chromosomal Replication.

<p>Data set was analyzed by the Ingenuity Pathways Analysis software (Ingenuity® Systems, <a href="http://www.ingenuity.com" target="_blank">www.ingenuity.com</a>). The color indicates the expression level of the genes (red indicating up-regulated genes and green indicating down-regulated genes).</p