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From the following article: An Introduction to the PANTHER Pathway Resource

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Figure 1a
Collapsed phylogenetic tree of a PANTHER protein family. PANTHER protein family PTHR19957, the Syntaxin family, is shown in the PANTHER TreeViewer. The phylogenetic tree was constructed computationally from sequence data. The collapsed tree shows the subfamilies as leaf nodes (blue diamond nodes). Subfamily nodes correspond to common ancestors of extant family members and are annotated, on the basis of experiments performed on extant proteins by expert biologists, with their inferred molecular functions and roles in biological processes and pathways. Each subfamily is represented by a hidden Markov model (HMM) to allow classification of newly discovered protein sequences.
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Figure 1b -

Figure 1b
Two subfamilies of the phylogenetic tree for the Syntaxin family—identified by the red arrow in (A)—are expanded to show Syntaxin 11 (SF30) and Syntaxin 4 (SF32) subfamily members, each spanning sequences from different vertebrates (zebrafish, mammals). Subfamilies can be expanded and collapsed by clicking on a node of the tree.
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Figure 1c -

Figure 1c
Multiple sequence alignment of a PANTHER protein family. Clicking on the "MSA" button shows the multiple sequence alignment (MSA) of the Syntaxin 11 and Syntaxin 4 subfamily member sequences, which is also used to build an HMM. Note that the MSA shows differences between amino acids conserved in different subfamilies (red arrows).
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Figure 2 -

Figure 2
PANTHER pathway module and its relationship to the PANTHER family/subfamily library module. A pathway molecule and molecular complex classes participate in a reaction, and a reaction is part of a pathway. Both pathways and molecule as well as complex classes are annotated with locations, either a cell type or cellular component. Since a reaction can span different cellular components (e.g., a transcription factor translocating from the cytosol to nucleus), the reaction itself is not annotated with a location. The pathway is linked to the PANTHER family/subfamily library module through the association of each pathway molecule class with one or more sequences in the library. Each sequence belongs to a subfamily, which indirectly links a pathway to a hidden Markov model (HMM), phylogenetic tree, and multiple sequence alignment (MSA).
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Figure 3a -

Figure 3a
Associating pathway molecule classes to subfamilies in a phylogenetic tree. Molecule class of GABA-B receptor (in yellow) in the GABA-B receptor II signaling pathway (PANTHER accession P05731).
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Figure 3b -

Figure 3b
Associating pathway molecule classes to subfamilies in a phylogenetic tree. The phylogenetic tree of GABA-B receptor. Subfamily 4 is the GABA-B receptor 2 (PANTHER accession PTHR10519:SF4), which is composed of sequences from human (red arrow), rat, insects, and worm
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Figure 4a -

Figure 4a
PANTHER Pathway home page text search. On the home page of PANTHER website, type the search term in the search box (blue arrow), and select "pathway" in the drop-down menu (red arrow). A list of pathways that contain the search term in the pathway class (or one of its associated molecule classes) will be returned.
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Figure 4b -

Figure 4b
Browse pathways using the PANTHER Prowler. Go to the PANTHER Prowler (http://www.pantherdb.org/panther/prowler.jsp) by clicking the "Browse" tab on the PANTHER home page. You can browse all PANTHER pathways together with other ontologies, such as molecular function and biological process. Simply clicking the "See Details" button will take you to the pathway diagram
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Figure 4c -

Figure 4c
Search by sequence. You can score a protein sequence against the PANTHER HMM library (http://www.pantherdb.org/tools/hmmScoreForm.jsp).
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Figure 5a -

Figure 5a
Process diagram (PD) view of a pathway. The Insulin-MAPK pathway (PANTHER accession P00032) is shown in the standard CellDesigner or PD view in PANTHER Pathway applet.
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Figure 5b -

Figure 5b
Activity flow (AF) view of a pathway. The Insulin-MAPK pathway is converted automatically to a Lite or AF diagram by the PANTHER Pathway applet.
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Figure 6a -

Figure 6a
Retrieve immediately upstream protein relationships captured in the pathways. The PANTHER Pathway applet utilizes relationships captured by the pathway and allows users to quickly and accurately retrieve the pathway component(s) immediately upstream of a protein by right-clicking a component and choosing "Select upstream".
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Figure 6b -

Figure 6b
Retrieve all pathway components upstream of a protein. Retrieve all pathway components upstream of a protein of interest by choosing "Select upstream path." The selected components are highlighted in yellow, and their gene, transcript, protein, or PANTHER family information can be retrieved.
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Figure 7a -

Figure 7a
PANTHER Gene Expression Analysis tools. PANTHER provides two tools for analyzing gene expression data: "Compare gene lists tool" and "Analyze a list of genes" with expression values (Mann-Whitney test).
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Figure 7b -

Figure 7b
The results from the Gene Expression Analysis Compare gene lists tool. The results of two sample gene lists were displayed in the p38 MAPK pathway (PANTHER accession P05918) using the PANTHER pathway applet. Components are shown in red and green if they are in one of the lists, in yellow if they are in both lists, and in gray if they are in neither list.
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Figure 7c -

Figure 7c
The results page from the Gene Expression Analysis Mann-Whitney test. By default, pathways are sorted by the Bonferroni-corrected P value comparing the distribution of values for the genes in the pathway to the overall distribution, with "+" indicating a shift toward higher values than overall and "-" indicating lower values. Clicking on the pathway name launches the pathway applet, as shown in Figure 7d.
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Figure 7d -

Figure 7d
Gene Expression Analysis Mann-Whitney test results are visualized in a pathway diagram of the p53 pathway (PANTHER accession P00059) using the PANTHER pathway applet that colors the pathway using a "heat map" derived from the input values. By default, the input values are divided into six quantiles (six bins, each with an equal number of data points); all genes in the lowest quantile are colored dark blue, with progressively warmer colors for higher-valued quantiles through to the highest quantile, which is colored red. The legend of the heat map can be found by clicking on the "Specify color ranges for pathway diagrams" button on the analysis result page as shown in Figure 7c, which also allows the user to customize the colors according to input value thresholds
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