PMC:539965 / 9503-11608
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/539965","sourcedb":"PMC","sourceid":"539965","source_url":"https://www.ncbi.nlm.nih.gov/pmc/539965","text":"DATA DISPLAY\nWhen searching DG-CST using the previously described ‘DNA-based’, ‘RNA-based’, ‘protein-based’, ‘advanced’ and ‘localization’ features, a list of CST entries that meet the search criteria can be accessed. Individual CSTs may be visualized in a specific page where all annotations available on that particular CST are displayed (Figure 2C). Matching CSTs from other species may be seen and compared in a multi-sequence alignment (Figure 2D). Matches found for each CST in a number of BLAST searches, pre-run against collections of genomic, EST or protein databases, may also be displayed starting from the CST page.\nOn the other hand, when searching by gene/disease name and/or symbol, it is possible to obtain a list of gene entries that meet the search criteria. Each gene entry, in addition to links to external resources such as LocusLink, ENSEMBL and OMIM, provides a ‘CST list’ link that gives access to the list of all CSTs found by analyzing the selected disease gene region, as shown in Figure 2A. By clicking on each entry, it is possible to access all the data pertaining to a given human CST, as described above.\nGraphical representation is accessible through a ‘map’ link, where CSTs and related annotations are shown within the context of the relative gene and its transcripts (Figure 2B). Moving through the genomic region and zooming to various levels of detail are supported. CSTs may be labeled by a color code on the basis of several quantitative parameters such as degree of human–mouse sequence identity, GC content, number of gaps, putative RNA secondary structures, palindromes and tandem repeats. To avoid an exceedingly crowded map, the graphic visualization tool allows the user to display selected CST subsets, such as: intergenic, intronic or exonic CSTs;CSTs containing putative TF binding sites;CSTs with matches to ESTs;CSTs conserved in additional species, besides human and mouse, such as chicken, fugu, zebrafish. These CSTs have a higher probability of representing functional elements playing a basic role in vertebrates as suggested by recent reports (23).","divisions":[{"label":"Title","span":{"begin":0,"end":12}}],"tracks":[{"project":"2_test","denotations":[{"id":"15608249-15131266-76718707","span":{"begin":2101,"end":2103},"obj":"15131266"}],"attributes":[{"subj":"15608249-15131266-76718707","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#99ec93","default":true}]}]}}