1 SEARCHING THE DB
In the query field it's possible to enter one of the following search keys:
1. Gene locus.
2. Network name.
3. A suitable string to search the annotation content.
The search can be performed by a gene view or a class view (by default, the gene view is selected).
Clicking on the Search button the query process starts.
2 RESULTS BY GENE VIEW
When the query process is ended, the list of loci associated to the query is shown. Each row of the list contains the information hereafter described.
GeneID: gene locus id. Clicking on the GeneID it is possible to browse the GeneID related page
Paralog: it shows the number of paralogs of the gene at the two different Evalue thresholds or zero in case of singletons or non protein-coding gene.
Class: the network name, if the gene has paralogs, or the name of the class if the gene is singleton or a non protein-coding gene.
The network name brings information on the network organization: the networks at the less stringent thresholds were named as NETxGy_z, where x indicates a number assigned when sorting the total amount of networks by decreasing network size; y indicates the network size (i.e. the number of included genes) and z is the number of networks or singletons in which the network is split when the more stringent cutoff is applied. The naming was established to keep a link between networks defined at the less conservative threshold and those at the more conservative one. Please note that each gene belongs to one and only one network at each threshold. For genes without paralogs, instead, the name of the class is reported. In case of unassigned genes, the classification field explains also the reasons of the unassignment, whereas for singleton genes the classification associated is reported too.
Net size: the number of all paralog genes contained into the network. Zero if the corresponding gene is a singleton or a non protein-coding gene.
Chr: the chromosome number on which the locus maps.
Start/End: starting/ending position of the locus on the chromosome.
Strand: forward or reverse strand of the chromosome.
Encoded transcript: the encoded transcript RefSeq. Each RefSeq has a link to the corresponding NCBI page.
Description: the annotation for each of the RefSeq.
3 RESULTS BY CLASS VIEW
When the query process is ended, the genes associated to the query are organized into classes, separating the genes not included in the network from those included in networks. It is possible to download the list of singletons detected by the query. Moreover the list of networks associated to the query is shown. Each row of the list contains the information hereafter described.
Network name: Clicking on the network name it is possible to browse the network related page
Sub Networks: it shows the number of sub networks or singletons in which the network is split when the cutoff of E<=10-10 is applied.
Network Size: it shows the number of genes included in the network.
Hits: it shows the number of hits found by the query.
Sub Network name: Clicking on the sub network name it is possible to browse the sub network related page
4 GeneID DETAILS AND NETWORK VISUALIZATION
When clicking on a GeneID name into the result table (gene view) all related information in terms of similar genes is reported in a new page. In particular:
4.1 In the topmost part of the page, near to the GeneID currently displayed, several lines summarize the information about the gene annotation and its possible association to networks.
4.2 In the bottom left part of the page the list of the GeneID paralogs is reported. For each paralog, the chromosome number with the start/end position and the description are reported. Please notice that the paralogs are directly linked to the Gene investigated while the network size can represent also genes not directly associated to the Gene under investigation. Clicking on a gene in the list, will crosslink the user to the newly selected GeneID details. It is also possible to download the list of paralogs or of all the genes included in the network by clicking on the corresponding links.
4.3 In the bottom center part of the page a network graph is reported. Each circle is a GeneID, with the light blue-circled one representing the selected GeneID and the yellow-circled one/s representing the paralog/s of the selected GeneID. Gray lines represent all the paralogy relationships included in the whole network, not necessarily paralogy relationships of the investigated GeneID.
5 NETWORK DETAILS
Clicking on a network name into the result table (network view) displays all its information in a new page. In particular:
5.1 In the left part of the page, the number of genes in the network is shown. The list of that genes is also reported.
5.2 In the right part of the page the network graph is reported.
PLEASE NOTE: For each network is possible to download the sif file from the link situated on the top of the picture (click on "Download this network in Cytoscape SIF file") so to facilitate the importing into Cytoscape. It is also possible to download the list of genes inside that network by clicking on "Download the gene list of this network".