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Tmm: Using the web interface to the database |
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Go back to the query interface The web interface provides a simple way to find coexpression links for a specific gene. Identifiers (Dbsource and ID fields): Not all genes are represented on microarrays, so if you fail to get any results, this could be the reason. If in doubt, find and use a probe identifier for a particular microarray. Here are the different kinds of identifiers Tmm understands.
StringencyEnter a small integer value here. This sets the number of data sets a link must be seen in before it is listed in the results. We recommend starting with a value of 3 for most human queries. However, if you are using a keyword that restricts the results to a smaller number of data sets, you may want to reduce this value. Try it and repeat the query with higher or lower values. Key wordsHere you can select a key word to restrict your search. The keywords are only listed if they are used in more than one data set. This feature is dependent on our meta data, which are still under development. Currently you can only use one key word at a time to limit your queries. On chipYou only need to use this option if you are entering a probe identifier in the "Dbsource" field. This is in fact optional as our system will try to find a matching probe if you enter the wrong array. This works because probe ids are (so far) unique. IdEnter the identifier here (gene name, etc.). Refseq60Check this box to limit your query to the data and genes used in the paper. Otherwise your query will be applied to the full set of genes in our database. Suppress visualizationsSkip presentation of the full data information. This can speed up your queries. Results pageThe results are presented in two formats: a table of genes, and a set of visualizations of the actual microarray data. Table of resultsThe main results section is a table listing the genes that your query were coexpressed with, given the criteria you set. The columns of this table include:
Getting text back outUse the "download results" link near the top of the page to download a text file that contains the tabulated results. This file can serve as a permanent record of your query. Example of data visualizationThese visualizations are only shown if you uncheck "suppress visualizations" on the query form. Light colors indicate higher expression. Grey indicates a missing value. ![]() |
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Paul Pavlidis. Last modified: Sat May 8 18:25:50 EDT 2004 |