The PANTHER site was designed to facilitate analysis of large numbers of genes, proteins or transcripts. For a more information about the data relationships, visit the "PANTHER Data Overview" figure.

Tools and data on the PANTHER site can be used to:

• Explore protein families, molecular functions, biological processes and pathways (section I).
• Generate lists of genes, proteins or transcripts that belong to a given protein family or subfamily, have a given molecular function or participate in a given biological process or pathway, e.g. generate a candidate gene list for a disease (section II).
• Analyze lists of genes, proteins or transcripts according to categories based on family, molecular function, biological process or pathway, e.g. analyze mRNA microarray data (section III).

Contents

I. Explore protein families, molecular functions, biological processes, and pathways.

I.A. Get information about a protein family or subfamily, and/or view a protein family phylogenetic tree and multiple sequence alignment.
I.B. Browse the PANTHER ontology of molecular functions, biological processes and pathways.
I.C. Explore pathways and the genes and proteins that participate in them.

II. Generate a list of genes, transcripts or proteins in PANTHER.

II.A. Create a list of genes with a given ontology association (molecular function, biological process, pathway).
II.B. Create a list of genes from a given family.
II.C. Create a list of genes in a genomic region.
II.D. Upload a list of IDs to the PANTHER site.
II.E. Create and order a list of Applied Biosystems Assays-on-Demand.

III. Analyze gene, protein or transcript lists by function.

III.A. Visualize a list of genes as a “pie chart“ broken down by gene function.
III.B. Analyze a list of genes in terms of statistically over- and -under-represented functions.
III.C. Analyze a list of gene-value pairs.

IV. Helpful Tips.

IV.A. Converting a list to another list type.
IV.B. Saving a list to your workspace.
IV.C. Exporting a list.
IV.D. Using the pie chart view.

Section I. Explore protein families, molecular functions, biological processes, and pathways.

I.A. Get information about a protein family or subfamily, and/or view a protein family phylogenetic tree and multiple sequence alignment.

1. Click on the “Families and HMMs” menu item, and click on the “Search for PANTHER families, trees and HMMs“.
2. Type search terms in the text box, and press the “Search“ button. Alternatively, you can search for PANTHER families via PANTHER ontology terms. After selecting the functions you are interested in (as outlined below in I.B), select “PANTHER Families“ in the box below the “Get Results“ button and press the button.
3. You will get a list of PANTHER families and subfamilies that matched the query.
4. Clicking on a family or subfamily identifier in the list will bring up the page for that family or subfamily, and that page contains links to the phylogenetic tree and multiple sequence alignment.

I.B. Browse the PANTHER ontology of molecular functions, biological processes and pathways.

1. Click on the “Ontologies” menu item.
2. Select the ontology you are interested in (left panel). Typing in the text field will filter the list of possible selections. Click on a “+“ to expand a category to view subcategories, and select categories by clicking on the checkbox next to the name. Brief details about each category can be seen by mousing-over a name, or full details by clicking on the icon to the left of a name. For pathways, full details include a detailed diagram of the molecular interactions and reactions in the pathway.
3. Selections can be made in more than one ontology. When multiple selections are made, it means that results will meet the criteria from all the selections. For example, one could select “Mouse“ from the species ontology as well as “Receptor“ from the molecular function ontology to retrieve all receptors in the mouse genome.
4. Review your selections in the Selection Summary panel.
5. Human curators have associated ontology terms with PANTHER families, subfamilies and “training sequences.“ To see these associations, select “PANTHER Families“ in the right panel and press the orange “Get Results“ button. Alternatively, you can also see the genes (in the selected species) that were hit by one of the family or subfamily HMMs by pressing the results button after selecting “Genes.“

I.C. Explore pathways and the genes and proteins that participate in them.

1. Retrieve a list of pathways using either the text search, or by browsing the list of available pathways in the Prowler (I.B.).
2. View the detailed information about a pathway by clicking on the pathway name or ID link in the pathway list, or by clicking on the icon to the left of the pathway name in the Prowler.
3. Select the “Pathway diagram“ tab on the Pathway Details page to view the interactive applet diagram. This diagram may take a few moments to load, especially for larger pathways.
4. Pathway “components“ (genes, mRNA, protein, small molecules) can be selected by clicking on them in the diagram, or by selecting them from the folder to the left of the diagram.
5. Genes, proteins or transcripts assigned to the selected components can be retrieved by pressing the “Go“ button at the top right of the pathway diagram.
6. Right-clicking on a pathway component allows a number of powerful features, such as highlighting all up- or downstream components, or displaying detailed information about a component.

Section II. Generate a list of genes, transcripts or proteins in PANTHER. These lists can always be used to find associated AB genomic assays (gene expression, SNP or resequencing) by clicking on the AB Assays button at the top of the list.

The PANTHER site was constructed to allow simple but powerful operations on a list of genes, proteins or transcripts. You can get to a PANTHER list view using a PANTHER search or browse, or by importing a list to the site. Once in the list view, a number of operations can be performed on the list. These operations are:

1. Viewing the list graphically as a pie or bar chart of gene functions. Click on the pie chart icon at the top of a list.
2. Saving a list to the Workspace. Choose “workspace“ from the “Send list to“ drop-down menu at the top of a list.
3. Exporting a list as a tab-delimited file. Choose “file“ from the “Send list to“ drop-down menu at the top of a list.
4. Sorting the list, e.g. to help find candidate genes. You can sort by protein family (click on the “PANTHER best hit“ column header), molecular function (click on the “molecular function“ column header) or biological process (click on the “biological process“ column header) etc.
5. Filtering the list to select only those entries with given search terms. Click on “refine search“ at the top of a list.
6. Converting the list to a different data type, e.g. convert a protein list to a list of all the genes that encode those proteins. Choose the new data type, from the “Convert list to“ drop-down menu.
7. Retrieving all of the Applied Biosystems Assays (Gene Expression, SNP or Resequencing) for the genes in the list. Click on “AB Genomic Assays“ link on the top right of the list.

II.A. Create a list of genes with a given ontology association (molecular function, biological process, pathway).

1. Click on the “Ontologies“ menu item.
2. Select the ontology you are interested in (left panel). Typing in the text field will filter the list of possible selections. Click on a “+“ to expand a category to view subcategories, and select categories by clicking on the checkbox next to the name. Brief details about each category can be seen by mousing-over a name, or full details by clicking on the icon to the left of a name.
3. Selections can be made in more than one ontology. For example, one could select “Mouse“ from the species ontology as well as “Receptor“ from the molecular function ontology to retrieve all receptors in the mouse genome.
4. Press the orange “Get Results“ button to retrieve genes by default (other result types can be selected first). Select the genome dataset genome(s) you want to search.

II.B. Create a list of genes from a given family.

1. Click on the “Families and HMMs“ menu item.
2. Type search terms in the text box, and press the “Go“ button. Alternatively, you can search for PANTHER families via PANTHER ontology terms. After selecting the functions you are interested in (as outlined above in I.A.), select “PANTHER Families“ in the box below the “Get Results“ button and press the button.
3. You will get a list of PANTHER families and subfamilies that matched the query.
4. Families and subfamilies of interest can be selected by clicking on the checkbox next to the ID. If no selections are made, all families and subfamilies are assumed to be selected.
5. Convert the list to a list of genes in the selected families/subfamilies by choosing “genes“ from the “Convert list to:“ drop-down menu.

II.C. Create a list of genes in a genomic region.

1. Click on “Genomes“ and then click on the “Location Search“ link.
2. Choose genome assembly.
3. To select the genomic region of interest, enter in the chromosomal coordinates, or the markers in the region of interest.
4. Set flanking region (the number of bases outside of the genomic region of interest) if desired. Press the “search“ button.
5. A list of genes will appear that match the genomic region.

II.D. Upload a list of IDs to the PANTHER site.

1. Go to the “batch upload“ page. You can access this page from the home page, from the “Genomes“ page, or from the Workspace by selecting the “new list“ link.
2. Each ID in your list of IDs should be separated by either a space, comma or carriage return character.
3. We recommend that you select the type of ID for a more precise lookup (select this under “select Upload ID type“ under Step 2 on the upload page). For genes, preferred IDs are Entrez Gene identifiers for public genes, Celera hCG identifiers for Celera genes.
4. You can select different types of objects to return (genes, transcripts, proteins) that match your uploaded IDs. Genes are the default object.
5. Choose “search“ under Step 2.
6. A gene list will appear that includes all of the recognized uploaded IDs.
7. You can view the unmapped IDs by clicking on the “Unmapped“ link at the top of the returned list.

II.E. Create and order a list of Applied Biosystems Assays-on-Demand.

1. Create a list of genes (or proteins or transcripts) from PANTHER ontology (II.A) or family (II.B) searches, or by uploading a list of identifiers to the site (II.C.).
2. You can review the list of genes and put a check mark next to only those that you select.
3. Once you have a gene list, you can convert it to a list of assays by choosing one of the assay types in the pull-down menu that appears when you mouse over the “View AB Assays“ text on the gene list.

Section III. Analyze gene, protein or transcript lists by function.

III.A. Visualize a list of genes as a “pie chart“ broken down by gene function.

1. Create a genelist as outlined in section II , or use the “batch upload“ page.
2. Select “MF pie chart“ (to categorize genes by molecular functions), “BP pie chart“ (to categorize genes by biological processes) or “Pathway pie chart“ from the pull-down menu under the pie chart icon. You can now use the pie chart view (IV.D.).

III.B. Analyze a list of genes in terms of statistically over- and -under-represented functions.

For example, you can correlate gene expression clusters with biological process (or molecular function) categories. This will allow you to look for statistically over- and under-represented biological processes among the genes in each cluster.

1. Click on the “Tools“ menu item, and then click on the “Gene Expression Data Analysis“ link, and then click on the “Lists of Genes“ link.
2. Follow the directions provided on the page. You will need to either upload the gene lists (II.D), or choose them from your workspace (IV.B).
3. You can analyze the list relative to molecular functions, biological processes or pathways, one at a time. To perform another analysis on the same data, just click on the back button of your browser.
4. When analyzing relative to pathway, clicking on the pathway name link will display the graphical pathway view with the genes/proteins in each list colored the same way.

III.C. Analyze a list of gene-value pairs.

For example, you can upload a list of genes and their corresponding fold-change values from a differential gene expression experiment. The values for the genes in each ontology category (e.g. the angiogenesis pathway) will be compared statistically to the overall distribution of values to look for coordinated shifts across that category. This approach has been used by our group (Clark et al., Science 302: 1960, 2003) and is similar to a method from Eric Lander’s group (Mootha et al., Nature Genetics 34: 267, 2003), to find weak coordinated shifts that elude methods such as III.B.

1. Click on the “Tools“ menu item, and then click on the “Gene Expression Data Analysis“ link, and then click on the “Lists of Genes with values“ link.
2. Follow the directions provided on the page. You will need to upload a tab-delimited file in which at least one column contains gene or protein identifiers (Entrez gene identifiers, GenBank accession numbers, or gene symbols), and at least one other column contains numerical values.
3. You can analyze the list relative to molecular functions, biological processes or pathways, one at a time. Press the “map genes to ontology“ button to launch the analysis. To perform another analysis on the same data, just click on the back button of your browser.
4. From the results page, you can view the distribution of values for each category, and how it compares to the overall distribution, by selecting the checkbox next to the category name, and then pressing the “Graph selected categories“ button.
5. For pathways, clicking on the pathway name link will display the graphical pathway view with genes/proteins colored by a hot-cold scale of the uploaded values (red is higher values).

Section IV. Helpful Tips.

IV.A. Converting a list to another list type.

1. When on a list page, click on the pull-down menu after “Convert list to:“. The current list type is shown in the box.
2. Select the new list type from the pull-down menu.
3. Each primary ID (first column of the list) is used to return the selected data type. Note that the mapping between different types is not necessarily one-to-one (e.g. a gene can map to more than one associated transcript).

IV.B. Saving a list to your workspace.

1. NOTE: this requires registration (register now for free; CDS customers use your CDS login and password)
2. From the list page, select “workspace“ in the “Send list to“ pull-down menu.
3. A pop-up window will ask you to name the list and add any comments. The name and comments can be edited at any time in the future from the Workspace page.
4. The gene list is now stored at the site, and can be returned to at any time. Only the IDs are stored, so when you access a list in the future, all information will be updated and current.

IV.C. Exporting a list.

1. From the list page, select “file“ in the “send list to:“ pull-down menu.
2. The list will be exported as a tab-delimited file.
3. You can now import the file into Excel or perform any post-processing you wish.

IV.D. Using the pie chart view. In this view, you can:

1. Make the pie chart larger or smaller. Choose a magnification percentage from the pull-down menu and press the “zoom“ button.
2. Convert to a bar chart view by clicking on “bar chart“.
3. View the category of a pie slice by putting the mouse over the slice.
4. Get a gene list for a particular slice of the pie by clicking on the name of the category in the legend.
5. View a more detailed breakdown of a category by clicking on a pie slice. For example, clicking on “Receptor“ will bring up a new pie chart in which the receptors are broken down by subtypes, e.g. “G protein-coupled receptor“ and “protein kinase receptor“.

About   |   Contact Us   |   System Requirements   |   Privacy Policy   |   Disclaimer
© Copyright 2007 SRI International. All Rights Reserved.