The comparison between intragenic and intergenic human L1s.

<p>(A) A bar graph shows 15 significant features passing the significance p-value 1.0E-03 (dashed line) from Mantel-Haenszel chi-square tests. The green and orange bars represent conserved and mutated features, respectively. These colored bars are aligned with L1 structure shown below the graphs. The bars marked with an asterisk (*) indicate the features calculated for the entire L1 sequence. (B) A bar graph shows non-categorical features whose significance p-value pass 1.0E-03 (dashed line). The blue columns indicate that more of these features appear in the intragenic L1s than that of intergenic ones. The red columns indicate that there are more of such features in the intergenic L1s than that of intragenic ones.</p

Intragenic L1s control gene expression in human early embryogenesis.

<p>Bold items indicate differential stages that pass the threshold (OR >1.0 and p-value <1.0E-03).</p><p>Intragenic L1s control gene expression in human early embryogenesis.</p

The comparison between intragenic and intergenic mouse L1s.

<p>(A) Bar graph of conserved (green columns) and mutated (orange columns) features from Mantel-Haenszel chi-square tests with cutoff of p-value <1.0E-03 (dashed line). The structure of mouse L1 is shown under the bar graph to indicate the relative location of the feature in L1 sequence. The bars marked with an asterisk (*) indicate the features calculated for the entire L1 sequence. (B) A bar graph shows significant non-categorical features with p-value <1.0E-03, using the Student's <i>t</i>-test. The blue columns indicate that more of these features appear in the intragenic L1s than that of intergenic ones. The red columns indicate that there are more of such features in the intergenic L1s than that of intragenic ones.</p

Distribution of mouse and human L1s over their genomes.

<p>(A) Graphical definition of intragenic and intergenic L1s. An intragenic L1 is represented by a blue box, while the intergenic one is represented in a red box. The black box represents a gene (intragenic region) and the black line represents an area outside (intergenic region) the gene bodies. (B) A bar graph shows the distribution of mouse (gray columns) and human (black columns) L1s residing on autosome, X, and Y-chromosomes. (C) Two side-by-side bar graphs comparing intragenic (blue columns) vs. intergenic (red columns) L1s on mouse and human genomes.</p

The down-regulated gene sets at differential gene expression stages in early embryogenesis that pass the chi-square tests.

<p>(A) Intersection of 4 gene sets in mouse genome. Each gene set is represented by a colored oval. The numbers in green, pink, yellow and blue ovals indicate the numbers of associated mouse genes in “2-cell vs. 1-cell”, “4-cell vs. 1-cell”, “8-cell vs. 1-cell”, and “morula vs. 1-cell” differential expressions stages, respectively. (B) Intersection of 3 gene sets in human genome. A colored circle represents each gene set. The numbers in yellow, blue, and red circles indicate the numbers of associated human genes in “8-cell vs. 1-cell”, “morula vs. 1-cell”, and “blastocyst vs. 1-cell” differential expression stages, respectively. (C) Name listing of mouse-human orthologous genes found in both mouse and human intersection gene sets. Each orthologous gene pair indicates the mouse gene name followed by the human gene name. The numbers in parentheses present the corresponding gene ids.</p

Roles of Intragenic and Intergenic L1s in Mouse and Human

<div><p>Long INterspersed Element-1 (LINE-1 or L1) is a retrotransposable element that has shaped the evolution of mammalian genomes. There is increasing evidence that transcriptionally active L1 could have been co-opted through evolution to play various roles including X-inactivation, homologous recombination and gene regulation. Here, we compare putatively active L1 distributions in the mouse with human. L1 density is higher in the mouse except for the Y-chromosome. L1 density is the highest in X-chromosome, implying an X-inactivation role. L1 is more common outside genes (intergenic) except for the Y-chromosome in both species. The structure of mouse L1 is distinguished from human L1 by the presence of a 200 bp repeat in the 5′ UTR of the former. We found that mouse intragenic L1 has significantly higher repeat copy numbers than intergenic L1, suggesting that this is important for control of L1 expression. Furthermore, a significant association between the presence of intragenic L1s and down-regulated genes in early embryogenesis was found in both species. In conclusion, the distribution of L1 in the mouse genome points to biological roles of L1 in mouse similar to human.</p></div

Intragenic L1s control gene expression in mouse early embryogenesis.

<p>Bold items indicate differential stages that pass the threshold (OR >1.0 and p-value <1.0E-03).</p><p>Intragenic L1s control gene expression in mouse early embryogenesis.</p

Search input and report output from the advanced search module.

<p>(A) The advanced search page is separated into three main parts. 1) A target gene or associated miRNA is put as a query. 2) The choices of binding site parameter settings can be adjusted to fit the user's needs. 3) The overlap of target site with specified annotated sequence is allowed as additional search criteria. (B) The list of resulting target sites obtained from search page is displayed. The information of associated miRNA is presented with the direction, chromosomal location, strand, length, upstream location, MFE, and conservation score of each target site including the number of bases with available score data. The number of different annotated sequences overlapping with each predicted target site is also shown. The hypertext link-outs to original sources of gene/miRNA associated information are provided. More target detail which includes a link to primer design is provided on the detail page of each target.</p

System overview of microPIR database.

<p>This is a three-tier system overview of the microPIR database displaying the data sources and web interface features.</p

Genome browser displaying the resulting target sites with other genomic features.

<p>The position of target site is presented in an integrated view along with other supporting information and genomic annotations on a local genome broswer. The region-level view shows the distribution of putative target sites located within a specified genomic region. Users can highlight (yellow color) to zoom in the interested location for the detail-level view. The target site is displayed in gold box with green line. The conservation score of each nucleotide position (blue color on the bottom) is displayed in the range from 0 to 1. AGO binding-site cluster is represented as distribution of read numbers along the cluster (green color). In this particular case, the presence of miRNA (red color) on the same locus as its binding site represents the <i>cis</i>-regulatory role of miRNA.</p