Organism : Methanococcus maripaludis S2 | Module List :
Regulation information for MMP0299(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Module neighborhood information for MMP0299
|Gene||Common Name||Description||Module membership|
|MMP0038||type II secretion system protein||115, 160|
|MMP0039||hypothetical protein MMP0039||115, 160|
|MMP0040||type II secretion system protein E||115, 160|
|MMP0041||tfb||transcription initiation factor IIB||19, 160|
|MMP0086||tfx||putative transcriptional regulator||150, 160|
|MMP0234||hypothetical protein MMP0234||46, 160|
|MMP0235||hypothetical protein MMP0235||75, 160|
|MMP0237||hypothetical protein MMP0237||75, 160|
|MMP0238||hypothetical protein MMP0238||160, 166|
|MMP0240||hypothetical protein MMP0240||75, 160|
|MMP0299||hypothetical protein MMP0299||154, 160|
|MMP0303||rubredoxin-type Fe(Cys)4 protein||30, 154|
|MMP0332||hypothetical protein MMP0332||30, 154|
|MMP0416||hypothetical protein MMP0416||30, 154|
|MMP0445||hypothetical protein MMP0445||30, 154|
|MMP0452||hypothetical protein MMP0452||75, 160|
|MMP0458||hypothetical protein MMP0458||75, 160|
|MMP0532||hypothetical protein MMP0532||30, 154|
|MMP0595||hypothetical protein MMP0595||75, 160|
|MMP0601||hypothetical protein MMP0601||30, 154|
|MMP0636||hypothetical protein MMP0636||75, 160|
|MMP0656||hypothetical protein MMP0656||46, 160|
|MMP0712||amino acid ABC transporter substrate-binding protein||58, 154|
|MMP0722||hypothetical protein MMP0722||58, 160|
|MMP0723||hypothetical protein MMP0723||75, 160|
|MMP0724||hypothetical protein MMP0724||30, 154|
|MMP0726||hypothetical protein MMP0726||30, 154|
|MMP0734||hypothetical protein MMP0734||30, 58, 154|
|MMP0753||hypothetical protein MMP0753||65, 154|
|MMP0754||hypothetical protein MMP0754||30, 154|
|MMP0783||hypothetical protein MMP0783||43, 160|
|MMP0798||hypothetical protein MMP0798||30, 154|
|MMP0826||hypothetical protein MMP0826||31, 154|
|MMP0827||hypothetical protein MMP0827||30, 154|
|MMP0846||hypothetical protein MMP0846||30, 154|
|MMP0944||hypothetical protein MMP0944||30, 154|
|MMP0972||hypothetical protein MMP0972||30, 154|
|MMP1276||hypothetical protein MMP1276||6, 154|
|MMP1279||camphor resistance protein CrcB||115, 160|
|MMP1608||hypothetical protein MMP1608||150, 160|
|MMP1632||yqiX||glutamate-binding protein||30, 154|
Gene Page Help
If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.
Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.
Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".
For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.
Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.
Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.
Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.
Module Members Tab
Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.
This help page. More general help can be accessed by clicking help menu in the main navigation bar.
CircVisOur circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
- 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
- 2. Source gene
- 3. Target genes (other module members)
- 4. Interactions between source and target genes for a particular module
- 5. Module(s) that source gene and target genes belong to
- 6. Visualisation legend
Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.
Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.
In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.