The parameters for computing the GNN and associated files are summarized in the table.
Uploaded Filename | 26150_IP91_IPR004184_NoFragments_Proteobacteria_UniRef90_NoFragments_IPR004184_Proteobacteria_Minlen650_AS240_full_ssn.xgmml.zip |
Neighborhood Size | 10 |
Input % Co-Occurrence | 20 |
Number of SSN clusters | 61 |
Number of SSN singletons | 40 |
SSN sequence source | UniRef90 |
Number of SSN (meta)nodes | 1,048 |
Number of accession IDs in SSN | 7,555 |
Each cluster in the submitted SSN has been identified and assigned a unique number and color. Node attributes for "Neighbor Pfam Families" and "Neighbor InterPro Families" have been added.
# Nodes | # Edges | File Size (Zipped MB) | |
---|---|---|---|
1,048 | 50,190 | 2 |
GNNs provide a representation of the neighboring Pfam families for each SSN cluster identified in the colored SSN. To be displayed, neighboring Pfams families must be detected in the specified window and at a co-occurrence frequency higher than the specified minimum.
Each hub-node in the network represents a SSN cluster. The spoke nodes represent Pfam families that have been identified as neighbors of the sequences from the center hub.
File Size (Zipped MB) | |
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2 |
Each hub-node in the network represents a Pfam family identified as a neighbor. The spokes nodes represent SSN clusters that identified the Pfam family from the center hub.
File Size (Zipped MB) | |
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3 |
Diagrams representing genomic regions around the genes encoded for the sequences from the submitted SSN are generated. All genes present in the specified window can be visualized (no minimal co-occurrence frequency filter or neighborhood size threshold is applied). Diagram data can be downloaded in .sqlite file format for later review in the View Saved Diagrams tab.
Action | File Size (Zipped MB) | |
---|---|---|
Opens GND explorer in a new tab. | ||
Diagram data for later review | 63 |
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