Mouse cursor; simply drag a rectangle around the chromosomal region of
Mouse cursor; simply drag a rectangle around the chromosomal region of interest either on the chromosome ideogram (HMPL-013 molecular weight Figure 3, button 1) or on individual data sets (Figure 3, buttons 7 and 9) and you will jump to that region. To orient yourPage 6 of(page number not for citation purposes)BMC Bioinformatics 2008, 9:http://www.biomedcentral.com/1471-2105/9/position relative to genes in the area, you can: (1) use the floating gene name box in the right column (Figure 3, button 3); (2) use the link to the UCSC Genome Browser; or (3) download the corresponding “Transcription” data with all gene names and positions.Downloading data for personal use For further analysis (an example is illustrated in Figure 4), you can download the data sets shown on your screen (Figure 4A). When this option is chosen, you will be prompted to select a location on your desktop for downloading all the data points for that data set contained within the selected genomic region. The data will bedownloaded as a tab-delimited text file that will contain a description of the data at the top, followed by a table of data that you can move into any spreadsheet program of choice for further analysis (Figures 4B, 4C and 4D). You can download data representing a small region or up to an entire chromosome using this function. If you desire the complete data set for all chromosomes, that is provided separately through the “Download Data” link in the main menu window (Figure 1, button 1). Of course, you may also save any web page as a .pdf or take a snapshot using your own computer if you want to build quick figures for group presentations.ABC D3 2 1 0 44000000 -1 -2 -3 Chromosome 8 Data Value_D3ESC Data Value_D3NPC NPC-ESC 44200000 44400000 44600000 44800000 45000000 45200000 45400000 45600000 45800000Figure PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27597769 4 An Exemplary Analysis Performed with ReplicationDomain An Exemplary Analysis Performed with ReplicationDomain. Visual inspection with the aid of ReplicationDomain identifies a region where replication timing has changed during differentiation of ESCs to NPCs. Users can download the data shown on the screen by selecting the “Save Data” option of each data set (A). Downloaded data for each data set will be in a tab-delimited text file with a description at the top (B). Data from multiple differentiation states can be assembled and their differentials calculated in Microsoft Excel (C) and visualized graphically (D). The graph (D) shows a comparison of D3ESC (dark blue) and D3NPC/EBM9 (green) replication timing profiles and their differentials (NPC-ESC; magenta) on chr8:44,000,000?46,000,000.Page 7 of(page number not for citation purposes)BMC Bioinformatics 2008, 9:http://www.biomedcentral.com/1471-2105/9/Comparing to other genome properties At the top of the page is a link entitled “UCSC Genome Browser for this Region” (Figure 3, button 5). Clicking this button will open a new tab or browser page to the UCSC Genome Browser for the region viewed on ReplicationDomain. In addition, if you wish to upload your own data sets and compare to other data sets on ReplicationDomain, you will need to register yourself first (see “Creating a ReplicationDomain account” below for details). Registered users are entitled to upload their data sets as described below under “Uploading your own data set.” Creating a ReplicationDomain account User registration is required for those who wish to upload their data sets or use the database interactively with other registered users. To create a Replicat.