Registration and Login

Access to GeneMesh™ requires registration. To register provide an email address (username) and password.

Creating a new project

To create a new project, click 'Add'. When the new screen loads, choose the type of the data to be uploaded from the 'Array Specification' pulldown. Provide a title and detailed description of the project. After submitting this information you will be able to upload multiple datasets into the newly created project folder.

Add a new data file (.CSV format) to a project

Select the project to which you want to upload a data file. Data files must be in the .CSV format.
Click "Open Selected Project" button to open the selected project.
Click "Upload a New Data File (.csv format)" button to reveal the file upload window.
Click "See example file" to see .CSV format.
Here, yellow highlighted line reminds you that the data being uploaded must correspond to the indicated chip type.
Click "Choose File" or " Browse" (depending on your web browser) button to choose a CSV file from your local computer.
Uploaded files will be listed in this table.

(A number of useful upfront operations on CSV formatted gene expression data including viewing of all genes in the data set with links to Entrez Gene summaries (using the ‘V’ action link), viewing of expression intensity values of genes in the data set (using the ‘VIV’ action link), grouping of genes in relation to gene ontologies (including biological processes, molecular functions and cellular components using the ‘B’, ‘M’ and ‘C’ action links, respectively), mapping of GeneIDs of individual genes or clusters of genes to KEGG pathway diagrams (using the ‘K’ action link) and generating heatmaps of expression intensities (using the ‘H’ action link). )

Toggle the radio button of the file that you want to work with.
Click "Use the Selected File" button to use the selected file.
The name of a selected file will appear in this area.
Click "Group Genes to MeSH Terms in a Specified MeSH Category" tab to group genes in the selected file according to MeSH categories or MeSH subcategories.
Click "Group Genes to MeSH Terms Associated with a Word/Phrase" tab to group genes in the selected file according to a specific term. Click on a major MeSH category to reveal subcategories.

Group genes in query set according to MeSH categories and MeSH terms

Click "Group Genes to MeSH Terms in a Specified MeSH Category" tab to group genes in the selected file according to MeSH categories or MeSH subcategories. Click on a major MeSH category to reveal subcategories.
Select GeneMesh Database Filter from pull down menu.

(GeneMesh allows the user to choose to employ different filters on the GeneMesh Database to govern inclusion of GeneIDs into MeSH categories. For example, using citation statistics, GeneIDs with greater than the average number of citations for a given MeSH category can be included by selecting ‘>Average’ from the pull down menu. This averaging is applied to all MeSH categories in the GeneMesh Database. Similarly, for each MeSH category in the GeneMesh Database, GeneIDs with greater than one standard deviation above the mean number of citations for a given MeSH category can be included by selecting the ‘>StDev’ pull down. The user may also employ an unfiltered form of the GeneMesh Database in which a GeneID is included in any given MeSH category if only a single citation refers to the corresponding gene in association with the category. This form of the database can be used by selecting ‘Unfiltered’ from the pull down menu.)

Output:
Total number of GeneIDs associated with this MeSH term.
Total number of Homologenes associated with this MeSH term.
Hypergeometric p value
Click 'B' to display biological process, 'M' to display molecular function ontology, 'C' cellular component
Click 'K' to view KEGG pathway diagrams for genes associated with a given MeSH category for the genes in the query set associated with this term.
Click 'N' to view protein interaction information displayed in a dynamically interactive network or 'T' to protein interaction information displayed in a tabular format
Click 'H' to display a heatmap of hybridization intensities of the genes from your query set associated with this term.

Group genes in your query set to MeSH subcategories associated with a specific term of your choice

Click "Group Genes to MeSH Terms Associated with a Word/Phrase" tab to group genes in the selected file according to a specific term.
Enter a search term and click the ‘Find’ button.
Select GeneMesh Database Filter from pull down menu.

(GeneMesh allows the user to choose to employ different filters on the GeneMesh Database to govern inclusion of GeneIDs into MeSH categories. For example, using citation statistics, GeneIDs with greater than the average number of citations for a given MeSH category can be included by selecting ‘>Average’ from the pull down menu. This averaging is applied to all MeSH categories in the GeneMesh Database. Similarly, for each MeSH category in the GeneMesh Database, GeneIDs with greater than one standard deviation above the mean number of citations for a given MeSH category can be included by selecting the ‘>StDev’ pull down. The user may also employ an unfiltered form of the GeneMesh Database in which a GeneID is included in any given MeSH category if only a single citation refers to the corresponding gene in association with the category. This form of the database can be used by selecting ‘Unfiltered’ from the pull down menu.)

Output:
Total number of GeneIDs associated with this MeSH term.
Total number of Homologenes associated with this MeSH term.
Hypergeometric p value
Click 'B' to display biological process, 'M' to display molecular function ontology, 'C' cellular component
Click 'K' to view KEGG pathway diagrams for genes associated with a given MeSH category for the genes in the query set associated with this term.
Click 'N' to view protein interaction information displayed in a dynamically interactive network or 'T' to protein interaction information displayed in a tabular format
Click 'H' to display a heatmap of hybridization intensities of the genes from your query set associated with this term.