EFI - Genome Neighborhood Tool

Results

Submitted Network Name: 29536_IPR004184_IP74_UniRef90_Minlen650_AS240_full_ssn

The parameters for computing the GNN and associated files are summarized in the table.

Uploaded Filename29536_IPR004184_IP74_UniRef90_Minlen650_AS240_full_ssn.xgmml
Neighborhood Size10
Input % Co-Occurrence10
Number of SSN clusters200
Number of SSN singletons196
SSN sequence sourceUniRef90
Number of SSN (meta)nodes4,178
Number of accession IDs in SSN16,274

Colored Sequence Similarity Network (SSN)

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)
4,178 1,187,272 29 MB

Genome Neighborhood Networks (GNNs)

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.

SSN Cluster Hub-Nodes: Genome Neighborhood Network (GNN)

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)
3 MB
Pfam Family Hub-Nodes Genome Neighborhood Network (GNN)

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)
6 MB

Genome Neighborhood Diagrams (GNDs)

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 42 MB

Mapping Tables, FASTA Files, ID Lists, and Supplementary Files

Mapping Tables
UniProt ID-Color-Cluster number 1 MB
Neighbor Pfam domain fusions at specified minimal co-occurrence frequency 3 MB
Neighbor Pfam domains at specified minimal co-occurrence frequency 4 MB
Neighbor Pfam domain fusions at 0% minimal co-occurrence frequency 9 MB
Neighbor Pfam domains at 0% minimal co-occurrence frequency 10 MB
Data Files per SSN Cluster
UniProt ID lists per cluster <1 MB
UniRef90 ID lists per cluster <1 MB
Neighbors without Pfam assigned <1 MB
Miscellaneous Files
No matches/no neighbors file <1 MB
Pfam family/cluster co-occurrence table file 2 MB
GNN hub cluster sequence count file <1 MB
Cluster size file <1 MB
SwissProt annotations per SSN cluster <1 MB
SwissProt annotations by singleton <1 MB

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