Pie chart of the predicted GOS protein clusters.

<p>The predicted GOS protein clusters are in three classes by similarities to existing protein sequences in NR: with homolog (BLASTP hits), with remote homolog (PDB-BLAST or FFAS hits), and novel (no hit). All matches to proteins in NR are considered in (a). Only matches to at least 20 non-redundant sequences in NR are included in (b).</p

Distribution of predicted GOS protein clusters within each sample.

<p>The <i>y</i>-axis is the number of clusters. In the upper figure, clusters are grouped and colored by the percentage of samples to which a cluster is associated. In the bottom figure, clusters are colored by novelty in terms of having homologs, remote homologs, or no homolog in known protein database.</p

Step-wise clustering of GOS ORFs.

<p>Step-wise clustering of GOS ORFs.</p

Distribution of clusters of GOS ORFs and NCBI NR proteins.

<p>The <i>x</i>-axis is the size of a cluster defined by the number of non-redundant sequences at 90% identity. Blue bars with numbers plotted against the left <i>y</i>-axis in log scale show the numbers of clusters. Red line plotted against right <i>y</i>-axis show the number of corresponding ORFs or sequences. Left is for GOS, and right is for NCBI NR.</p

Distribution of predicted GOS protein clusters by their associated samples.

<p>The <i>x</i>-axis is the cluster size; the <i>y</i>-axis is the number of a cluster's associated samples. The pie chart inset shows distribution of clusters by the percentage of samples to which a cluster is associated.</p

Distribution of ORFs by length.

<p>The <i>x</i>-axis is the length bin of ORFs. The <i>y</i>-axis is number of ORFs in two groups: ORFs in predicted protein clusters and other ORFs.</p

Distribution of clusters by their associated organisms and functional classes.

<p>The left figure shows the number of clusters by organisms at the level of main domains of life (Archea, Eucaryota, Bacteria, and Viral). For example, “A,B” means a cluster has only Archaea and Bacteria homologs. The right figure shows distributions by COG functional classes. Blue bars plotted against left <i>y</i>-axis show numbers of clusters. Red and green lines plotted against right <i>y</i>-axis are numbers of GOS ORFs and the underlying COG sequences multiplied by 40 for scaling. COG functional classes are: C, energy; D, cell division, chromosome partitioning; E, amino acid; F, nucleotide; G, carbohydrate; H, coenzyme; I, lipid; J, translation, ribosomal structure, and biogenesis; K, transcription; L, DNA replication, recombination, and repair; M, cell wall/membrane/envelope; N, cell motility and secretion; O, posttranslational modification, protein turnover, chaperones; P, inorganic ion; Q, secondary metabolites; R, general function prediction only; S, function unknown; and T, signal transduction.</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 biologically relevant pathways: Regulation of the cell cycle: The G1/S checkpoint control.

<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

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