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LitInspector allows input of gene synonyms or gene IDs and free text. At least one gene synonym or free text word or phrase has to be submitted. The query, in addition, can be filtered for only those abstracts for which also defined keyword categories (tissue, disease, or pathway) were identified.
| Input parameters | |
|---|---|
| Enter gene name or gene ID | Enter a single gene symbol or the full gene name or any valid gene synonym. Example: WT1 or wt 1 or Wilms tumor 1 will be identified as the gene with gene ID 7490. You can also directly enter the gene ID like 7490. Case sensitivity is not required. Dashes (-) in gene names as in WT-1 are not necessary and interpreted as blanks like in WT 1. Wildcards are allowed (WT* or *WT*). Please note that the entered gene name has to consist of more than two letters or numbers. If the entered gene name is ambiguous (e.g. a homonym) an intermediate page will open where you can select the right gene. You have the possibility to enter up to three different genes. The genes can be combined with AND or OR (please use capital letters; default is AND). |
| Organism | Select an organism from the pop up menu. The default organism is Homo sapiens. |
| Free text search |
Enter a search term like liver or a phrase like liver disease. Different search terms can be combined using the boolean operators OR/AND (capital letters). Example: liver OR hepatic AND disease. Please do not type wildcards, parentheses, or quotation marks. |
| Filter for MeSH Term classifiers |
Check for presence of keyword categories assigned to MeSH Terms. Available categories are tissue and disease. |
| Filter for classifiers in the abstarct |
Check for presence of keyword categories occurring in the abstract. Available categories are tissue, disease, and pathway. Please note: in case of free text searches, only sentences containing a keyword from the selected category are shown. |
| Highlight in the output |
Define which keywords will be highlighted in the output. Per default, transcription factors and genes are highlighted. The following keyword categories are available:
Note: If a filter for classifiers in the abstract (Tissue, Disease, or Pathway) is selected, the corresponding highlighting is automatically enabled. Please also note that this feature is only available when LitInspector is started from the GenomatixPortal main menu. |
If the entered gene synonym is unique (example: WT1), LitInspector directly opens a page with the Query Info and the Results. The Results are all sentences of the abstract in which the query gene was identified. A maximum of 100 abstracts is shown on one results page, in case of further matches these are available using the "Next Page" button.
If the entered synonym is a homonym, i.e. one and the same synonym is used for two or more different genes (example: MBP), an intermediate page will open and the user can select the demanded gene(s).
Example:
If the entered synonym cannot be found in the database, LitInspector will automatically perform a wildcard search, adding the wildcard at the end of the entered gene name (example: PAX -> PAX*). If still no gene can be assigned to the entered synonym, the best way is to try the gene ID directly.
It is also possible to scan for two or three different genes. Please use the separate form fields for each single gene. In this case an intermediate page will open; please select the relevant genes using the checkboxes and choose the radio button for boolean OR or AND combination of the different query genes.
Example:
Enter "WT1" in the first form field and "PAX" in the second form field. In the intermediate page you can select "WT1" as gene number one and "PAX2" as gene number two. If you choose the radio button "AND connection between different selected genes" (default), the LitInspector result will show only papers where WT1 and PAX2 are tagged in the same abstract.
Gene searches and free text searches can be combined. Example: "WT1" is entered in the gene form field together with "kidney development OR renal development" in the free text field. The result will show all abstract sentences where the gene WT1 was tagged and the phrase ("kidney development" OR "renal development") was found in the same abstract.
Please note that in contrast to genes or keywords free text search terms are not automatically highlighted and do not necessarily occur in the selection of sentences shown in the LitInspector results page. The reason for that is, that only sentences containing also tagged genes or keywords are shown in the results. If the free text search phrase is in a sentence that does not contain a tagged word, the sentence is not shown in the output. However, it is contained in the abstract which can be proven by following the NCBI PubMed link.
The following links to further results for your gene are available:
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Analyse gene relation networks |
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Genome annotation browser |
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Transcription factor knowledge base |
The statistics shows how many PubMed abstracts were scanned in the current analysis (absolute and in percent from complete PubMed). In addition, the total number of PubMed abstracts in the database is given as well as the the number of abstracts found so far. Each LitInspector output page contains a maximum of 100 abstracts. If further matches are available, they can be retrieved by pressing the "Next Page" button. In case the complete PubMed has been scanned, this information is displayed at the bottom of the statistics.
The "Get Selected Abstracts" button generates a link to all publications manually selected using the check boxes in front of the journal titles in the LitInspector result page. You can choose between the LitInspector format with the color coded sentences or a direct link to the NCBI PubMed abstracts.Genomatix Signal Transduction Pathways are obtained by literature data mining based on all available PubMed abstracts. The output table lists the pathway associations identified for the entered gene ordered by the number of references (column "Ref."), i.e. PubMed abstracts. By clicking the number you get access to the references as color coded sentences in LitInspector format (the link is limited to the newest 100 abstracts). The Pathway Component specifies the signaling element that was identified to be associated with your entered gene. The pathway components themselves are assigned to Signaling Pathways. To get an overview, most pathways are referenced by a graphical representation, referring to BioCarta, STKE, or KEGG.
Output example:
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