NetworkComparer - find conserved co-expression networks in different species
NetworkComparer tool permits comparative analysis of co-expression networks across seven plant species: Arabidopsis, barley, Medicago, poplar, rice, soybean and wheat. The tool can be applied to infer conserved co-expression relationships in the seven species, which can be used to predict most likely functional homologs and to infer novel participants of investigated biological process. Go to FAQ section for elaborated explanation of how the NetworkComparer tool works.
You can commence the analysis using two methods:
Standard analysis
You can commence the analysis using two methods:
- Standard analysis accepts your gene of interest and compares it to other genes belonging to the PFAM family of the query.
- User defined probeset analysis accepts several, user-defined genes for analysis.
Standard analysis
- Enter a keyword, probeset ID or transcript ID into the box below and click Search.
- This tool will then search the PlaNet database for probesets matching the search term. Next page will display probeset found by the keyword. Select one probeset which will then be used as query for the analysis.
- The tool will then compare all members associated with the PFAM family that the query probeset belongs to.
- The comparison returns a Similarity Network and a table that displays similarity scores between the NVN of the query probeset and NVNs of members of the pfam of the query.
- Select the interesting, highly scoring probesets.
- These probesets are then used to generate the Ancestral Network, which depicts conserved co-expression relationships across selected probesets. Resulting table also reveals the identity of transcripts constituting conserved PFAMs.
User-specified analysis
- Enter a keyword, probeset ID or transcript ID into the box below and click Search.
- This tool will then search the PlaNet database for probesets matching the search term. Next page will display probeset found by the keyword. Select probesets which will then be used as query for the analysis.
- The tool will then compare all selected probesets.
- The comparison returns a Similarity Network and a table that displays similarity scores between the NVNs of selected probesets.
- Select the interesting, highly scoring probesets.
- These probesets are then used to generate the Ancestral Network, which depicts conserved co-expression relationships across selected probesets. Resulting table also reveals the identity of transcripts constituting conserved PFAMs.
Manually specify two neighborhoods for comparison.
With this tool you can manually assign genes to modules. PlaNet will compare the modules and highlight module similarities.
Example:
at3g03050 1
at4g32410 2
at5g64740 2
This will assign at3g03050 to group 1. at4g32410 and at5g64740 are assigned to group 2. The groups will then be assessed for conservation of gene families.
With this tool you can manually assign genes to modules. PlaNet will compare the modules and highlight module similarities.
Example:
at3g03050 1
at4g32410 2
at5g64740 2
This will assign at3g03050 to group 1. at4g32410 and at5g64740 are assigned to group 2. The groups will then be assessed for conservation of gene families.
Specifying modules
With this tool you can find co-expression network regions that contain gene families/protein domains (labels) that you specified.
You can specify your query by using label names (e.g. Cellulose_synt!, COBRA, Pkinase) or by gene names (e.g. at4g32410!, at5g60920, at5g01020).
You can use comma-separated or line-separated entry. Also, if there is a given label that must always be present in the found regions, place ! next to the gene/label, as done for the Cellulose_synt and at4g32410! in above example.
With this tool you can find co-expression network regions that contain gene families/protein domains (labels) that you specified.
You can specify your query by using label names (e.g. Cellulose_synt!, COBRA, Pkinase) or by gene names (e.g. at4g32410!, at5g60920, at5g01020).
You can use comma-separated or line-separated entry. Also, if there is a given label that must always be present in the found regions, place ! next to the gene/label, as done for the Cellulose_synt and at4g32410! in above example.