The transcripts section allows to search for several transcripts features, annotations and functional characterization.
Furthermore it is possible to set an expression threshold and filter for transcripts with a detected peptide.
Choose a search object from one of the search sections:
- Transcript centered search, which refers to Transcript features like length or name of transcript
- Annotation centered search, which refers to annotation features like significance (eValue) or "free text search in annotations"
- Functional Annotation centered search allows to search for functional identifiers like GO terms or Interpro ids
First you need to add the search object to your query by clicking "add selected field". Besides the dropdown list of the search object a logical operator select field is located.
The operator (AND or OR) will be applied to all search fields of a section. Depending on your selection the entities will be combined in a search (AND), or seen as single entities in a query (OR).
Each field has an infield label which refers to the input format. By navigating the mouse over a field you will get further information on that particular search field.
Filtering your search
Underneath the Functional search section two filters are located to refine the results of your query by choosing
- Only deregulated transcripts (first checkbox)
- Only transcripts with at least one identified peptide (second checkbox)
- Transcripts, which are deregulated and have at least one identified peptide (both checkboxes)
The threshold for your fold change can be choosen from the dropbox. Please note, that a scan for peptides in combination with a complex query can take several minutes.
On the bottom of the transcripts search it is possible to choose between a "classical result output" and a "smart result view". Furthermore it is possible to use a search status and query filter. The query filter will show additional information referring to your search, the output and the entity information. For large searches it is recommended to use the smart result view. Please keep in mind, that the smart search tool is still beta and under construction. The smart search output view allows for free text search, sorting and filtering the results in smart data tables. The classical view is faster and gives the opportunity for quick check of alignments.
The results page
The results page is divided in three parts:
- Overview of the query
- Detailed results overview
- If a search in the annotation section is performed an additional Overview of annotation search is shown.
The Overview of the query will list your query input and the number of hits in transcripts, annotations, GO annotation and other functional annotations.
The Detailed results overview is divided due to the three section the search was performed in.
- Annotation results
View of transcript id, transcript name, number of ests in transcript, length of sequence, blast result and alignment (mouse over) and significance.
- Transcript results
View of transcript id, transcriptname, number of ests in transcript, length of sequence, blast result and alignment (mouse over) and significance.
- Functional annotation results
View of transcript id, transcriptname, number of ests in transcript, length of sequence, uniprot id, pathway, interpro id, GO term and go term name.